From 61e9e629252213bad70f5c7a152e21a22ba1db1e Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Tue, 7 Jul 2015 12:48:43 +0100
Subject: [PATCH] Added new functionality for output pdb in analysis
You can now use COLLECT_FRAMES to collect pdb data from the trajectory
and output a pdb file that contains the underlying atomic coordinates
in pdb format even if you are not using the rmsd distance to measure
the dissimilarity matrix for dimensionality reduction. Also fixed
a number of bugs.
---
regtest/analysis/rt-calc-dissims2/Makefile | 1 +
regtest/analysis/rt-calc-dissims2/config | 4 +
regtest/analysis/rt-calc-dissims2/plumed.dat | 7 +
regtest/analysis/rt-read-dissims2/plumed.dat | 4 +-
regtest/dimred/Makefile | 2 +
regtest/dimred/rt-mds2/Makefile | 1 +
.../dimred/rt-mds2/analysis.0.embed.reference | 1200 +++++++++++++++++
.../rt-mds2/analysis.0.list_embed.reference | 101 ++
regtest/dimred/rt-mds2/config | 2 +
regtest/dimred/rt-mds2/embed.reference | 1200 +++++++++++++++++
regtest/dimred/rt-mds2/in | 11 +
regtest/dimred/rt-mds2/input.xyz | 9 +
regtest/dimred/rt-mds2/list_embed.reference | 101 ++
regtest/dimred/rt-mds2/plumed.dat | 30 +
src/analysis/AnalysisBase.cpp | 2 +-
src/analysis/AnalysisBase.h | 7 -
src/analysis/AnalysisWithDataCollection.cpp | 113 +-
src/analysis/AnalysisWithDataCollection.h | 9 +-
src/analysis/EuclideanDissimilarityMatrix.cpp | 13 +-
src/analysis/ReadAnalysisFrames.cpp | 10 +-
src/analysis/ReadDissimilarityMatrix.cpp | 15 +-
src/dimred/DimensionalityReductionBase.cpp | 6 +-
src/dimred/DimensionalityReductionBase.h | 1 -
src/dimred/ProjectNonLandmarkPoints.cpp | 7 +-
src/dimred/SketchMapBase.cpp | 2 +-
src/dimred/SketchMapBase.h | 6 +-
src/dimred/SketchMapPointwise.cpp | 45 +-
src/dimred/SketchMapSmacof.cpp | 14 +-
src/reference/MultiDomainRMSD.cpp | 2 +
src/reference/OptimalRMSD.cpp | 2 +-
src/reference/ReferenceAtoms.cpp | 1 +
src/reference/ReferenceConfiguration.cpp | 8 +
src/reference/ReferenceConfiguration.h | 1 +
33 files changed, 2794 insertions(+), 143 deletions(-)
create mode 100644 regtest/analysis/rt-calc-dissims2/Makefile
create mode 100644 regtest/analysis/rt-calc-dissims2/config
create mode 100644 regtest/analysis/rt-calc-dissims2/plumed.dat
create mode 100644 regtest/dimred/Makefile
create mode 100644 regtest/dimred/rt-mds2/Makefile
create mode 100644 regtest/dimred/rt-mds2/analysis.0.embed.reference
create mode 100644 regtest/dimred/rt-mds2/analysis.0.list_embed.reference
create mode 100644 regtest/dimred/rt-mds2/config
create mode 100644 regtest/dimred/rt-mds2/embed.reference
create mode 100644 regtest/dimred/rt-mds2/in
create mode 100644 regtest/dimred/rt-mds2/input.xyz
create mode 100644 regtest/dimred/rt-mds2/list_embed.reference
create mode 100755 regtest/dimred/rt-mds2/plumed.dat
diff --git a/regtest/analysis/rt-calc-dissims2/Makefile b/regtest/analysis/rt-calc-dissims2/Makefile
new file mode 100644
index 000000000..3703b27ce
--- /dev/null
+++ b/regtest/analysis/rt-calc-dissims2/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/analysis/rt-calc-dissims2/config b/regtest/analysis/rt-calc-dissims2/config
new file mode 100644
index 000000000..4804b7f2a
--- /dev/null
+++ b/regtest/analysis/rt-calc-dissims2/config
@@ -0,0 +1,4 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%8.4f"
+extra_files="../../trajectories/trajectory.xyz"
diff --git a/regtest/analysis/rt-calc-dissims2/plumed.dat b/regtest/analysis/rt-calc-dissims2/plumed.dat
new file mode 100644
index 000000000..f8ce0f6b2
--- /dev/null
+++ b/regtest/analysis/rt-calc-dissims2/plumed.dat
@@ -0,0 +1,7 @@
+d1: DISTANCE ATOMS=1,2
+d2: DISTANCE ATOMS=3,4
+
+c1: COLLECT_FRAMES ATOMS=1-20 STRIDE=1
+r1: EUCLIDEAN_DISSIMILARITIES FRAMES=c1 ARG=d1,d2
+l1: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=r1 NLANDMARKS=5
+OUTPUT_ANALYSIS_DATA_TO_PDB USE_OUTPUT_DATA_FROM=l1 FILE=configs-stride.pdb FMT=%8.4f
diff --git a/regtest/analysis/rt-read-dissims2/plumed.dat b/regtest/analysis/rt-read-dissims2/plumed.dat
index 313bb905b..9092819cb 100644
--- a/regtest/analysis/rt-read-dissims2/plumed.dat
+++ b/regtest/analysis/rt-read-dissims2/plumed.dat
@@ -1,6 +1,6 @@
-c1: READ_ANALYSIS_FRAMES ATOMS=1-20 STRIDE=1
+c1: COLLECT_FRAMES ATOMS=1-20 STRIDE=1
-r1: READ_DISSIMILARITY_MATRIX TRAJ=c1 FILE=mymatrix.dat
+r1: READ_DISSIMILARITY_MATRIX FRAMES=c1 FILE=mymatrix.dat
PRINT_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=r1 FILE=mymatrix_out.dat FMT=%8.4f
l1: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=r1 NLANDMARKS=5
diff --git a/regtest/dimred/Makefile b/regtest/dimred/Makefile
new file mode 100644
index 000000000..42480767a
--- /dev/null
+++ b/regtest/dimred/Makefile
@@ -0,0 +1,2 @@
+include ../scripts/module.make
+
diff --git a/regtest/dimred/rt-mds2/Makefile b/regtest/dimred/rt-mds2/Makefile
new file mode 100644
index 000000000..3703b27ce
--- /dev/null
+++ b/regtest/dimred/rt-mds2/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/dimred/rt-mds2/analysis.0.embed.reference b/regtest/dimred/rt-mds2/analysis.0.embed.reference
new file mode 100644
index 000000000..8403111e2
--- /dev/null
+++ b/regtest/dimred/rt-mds2/analysis.0.embed.reference
@@ -0,0 +1,1200 @@
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0873 mds.2=0.0013
+ATOM 1 X RES 0 0.295 -1.126 0.000 0.14 0.14
+ATOM 2 X RES 1 0.731 0.874 0.000 0.14 0.14
+ATOM 3 X RES 2 0.003 -0.026 0.000 0.14 0.14
+ATOM 4 X RES 3 1.122 -0.139 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.336 1.085 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.712 -0.919 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.103 0.252 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0535 mds.2=0.0044
+ATOM 1 X RES 0 0.321 -1.135 0.000 0.14 0.14
+ATOM 2 X RES 1 0.743 0.904 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.002 -0.023 0.000 0.14 0.14
+ATOM 4 X RES 3 1.102 -0.153 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.323 1.092 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.739 -0.939 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.101 0.254 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0150 mds.2=0.0044
+ATOM 1 X RES 0 0.359 -1.136 0.000 0.14 0.14
+ATOM 2 X RES 1 0.755 0.925 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.001 -0.015 0.000 0.14 0.14
+ATOM 4 X RES 3 1.067 -0.164 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.321 1.092 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.770 -0.946 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.089 0.244 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0136 mds.2=0.0019
+ATOM 1 X RES 0 0.394 -1.132 0.000 0.14 0.14
+ATOM 2 X RES 1 0.767 0.936 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.007 -0.003 0.000 0.14 0.14
+ATOM 4 X RES 3 1.024 -0.170 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.329 1.092 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.779 -0.944 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.070 0.222 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0308 mds.2=-0.0012
+ATOM 1 X RES 0 0.422 -1.125 0.000 0.14 0.14
+ATOM 2 X RES 1 0.777 0.940 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.031 0.005 0.000 0.14 0.14
+ATOM 4 X RES 3 0.994 -0.175 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.330 1.081 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.771 -0.931 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.061 0.204 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0355 mds.2=-0.0018
+ATOM 1 X RES 0 0.445 -1.115 0.000 0.14 0.14
+ATOM 2 X RES 1 0.787 0.935 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.055 0.002 0.000 0.14 0.14
+ATOM 4 X RES 3 0.991 -0.172 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.339 1.072 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.758 -0.908 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.070 0.186 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0090 mds.2=-0.0015
+ATOM 1 X RES 0 0.454 -1.106 0.000 0.14 0.14
+ATOM 2 X RES 1 0.789 0.917 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.053 -0.012 0.000 0.14 0.14
+ATOM 4 X RES 3 1.007 -0.158 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.346 1.064 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.746 -0.876 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.104 0.173 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0145 mds.2=0.0004
+ATOM 1 X RES 0 0.459 -1.086 0.000 0.14 0.14
+ATOM 2 X RES 1 0.780 0.899 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.042 -0.033 0.000 0.14 0.14
+ATOM 4 X RES 3 1.034 -0.145 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.355 1.055 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.727 -0.857 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.148 0.168 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0191 mds.2=0.0022
+ATOM 1 X RES 0 0.454 -1.056 0.000 0.14 0.14
+ATOM 2 X RES 1 0.766 0.880 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.035 -0.042 0.000 0.14 0.14
+ATOM 4 X RES 3 1.072 -0.140 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.369 1.033 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.701 -0.848 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.187 0.173 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0278 mds.2=0.0015
+ATOM 1 X RES 0 0.434 -1.026 0.000 0.14 0.14
+ATOM 2 X RES 1 0.737 0.865 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.013 -0.025 0.000 0.14 0.14
+ATOM 4 X RES 3 1.123 -0.149 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.385 1.010 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.684 -0.858 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.212 0.183 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0091 mds.2=-0.0004
+ATOM 1 X RES 0 0.401 -0.995 0.000 0.14 0.14
+ATOM 2 X RES 1 0.705 0.855 0.000 0.14 0.14
+ATOM 3 X RES 2 0.016 0.001 0.000 0.14 0.14
+ATOM 4 X RES 3 1.177 -0.161 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.405 0.986 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.674 -0.872 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.220 0.185 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0359 mds.2=-0.0012
+ATOM 1 X RES 0 0.384 -0.972 0.000 0.14 0.14
+ATOM 2 X RES 1 0.679 0.843 0.000 0.14 0.14
+ATOM 3 X RES 2 0.039 0.030 0.000 0.14 0.14
+ATOM 4 X RES 3 1.220 -0.177 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.430 0.968 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.673 -0.877 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.219 0.185 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0540 mds.2=0.0004
+ATOM 1 X RES 0 0.384 -0.963 0.000 0.14 0.14
+ATOM 2 X RES 1 0.670 0.847 0.000 0.14 0.14
+ATOM 3 X RES 2 0.048 0.038 0.000 0.14 0.14
+ATOM 4 X RES 3 1.245 -0.197 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.458 0.969 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.685 -0.867 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.206 0.173 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0322 mds.2=-0.0034
+ATOM 1 X RES 0 0.392 -0.967 0.000 0.14 0.14
+ATOM 2 X RES 1 0.684 0.880 0.000 0.14 0.14
+ATOM 3 X RES 2 0.039 0.023 0.000 0.14 0.14
+ATOM 4 X RES 3 1.266 -0.216 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.487 0.985 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.708 -0.852 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.186 0.146 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0205 mds.2=-0.0150
+ATOM 1 X RES 0 0.411 -0.983 0.000 0.14 0.14
+ATOM 2 X RES 1 0.688 0.924 0.000 0.14 0.14
+ATOM 3 X RES 2 0.020 -0.000 0.000 0.14 0.14
+ATOM 4 X RES 3 1.281 -0.230 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.508 1.006 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.730 -0.844 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.161 0.127 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0282 mds.2=-0.0289
+ATOM 1 X RES 0 0.438 -1.014 0.000 0.14 0.14
+ATOM 2 X RES 1 0.672 0.964 0.000 0.14 0.14
+ATOM 3 X RES 2 0.005 -0.011 0.000 0.14 0.14
+ATOM 4 X RES 3 1.293 -0.237 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.528 1.029 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.745 -0.846 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.134 0.115 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0530 mds.2=-0.0358
+ATOM 1 X RES 0 0.462 -1.044 0.000 0.14 0.14
+ATOM 2 X RES 1 0.646 0.996 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.003 -0.016 0.000 0.14 0.14
+ATOM 4 X RES 3 1.303 -0.232 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.545 1.058 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.754 -0.876 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.110 0.114 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0769 mds.2=-0.0312
+ATOM 1 X RES 0 0.485 -1.067 0.000 0.14 0.14
+ATOM 2 X RES 1 0.615 1.013 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.006 -0.012 0.000 0.14 0.14
+ATOM 4 X RES 3 1.307 -0.223 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.546 1.082 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.753 -0.924 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.102 0.131 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0893 mds.2=-0.0259
+ATOM 1 X RES 0 0.493 -1.082 0.000 0.14 0.14
+ATOM 2 X RES 1 0.582 1.016 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.004 -0.005 0.000 0.14 0.14
+ATOM 4 X RES 3 1.308 -0.216 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.524 1.102 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.751 -0.963 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.105 0.149 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0697 mds.2=-0.0246
+ATOM 1 X RES 0 0.490 -1.087 0.000 0.14 0.14
+ATOM 2 X RES 1 0.550 1.015 0.000 0.14 0.14
+ATOM 3 X RES 2 0.004 -0.009 0.000 0.14 0.14
+ATOM 4 X RES 3 1.300 -0.213 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.501 1.110 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.739 -0.981 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.104 0.165 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0302 mds.2=-0.0196
+ATOM 1 X RES 0 0.481 -1.082 0.000 0.14 0.14
+ATOM 2 X RES 1 0.536 1.002 0.000 0.14 0.14
+ATOM 3 X RES 2 0.016 -0.008 0.000 0.14 0.14
+ATOM 4 X RES 3 1.276 -0.209 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.491 1.105 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.723 -0.982 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.096 0.175 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0093 mds.2=-0.0072
+ATOM 1 X RES 0 0.474 -1.070 0.000 0.14 0.14
+ATOM 2 X RES 1 0.558 0.978 0.000 0.14 0.14
+ATOM 3 X RES 2 0.032 -0.010 0.000 0.14 0.14
+ATOM 4 X RES 3 1.233 -0.205 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.506 1.090 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.708 -0.963 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.084 0.180 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0274 mds.2=0.0009
+ATOM 1 X RES 0 0.471 -1.054 0.000 0.14 0.14
+ATOM 2 X RES 1 0.591 0.949 0.000 0.14 0.14
+ATOM 3 X RES 2 0.042 -0.017 0.000 0.14 0.14
+ATOM 4 X RES 3 1.184 -0.200 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.528 1.080 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.695 -0.934 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.066 0.176 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0301 mds.2=0.0016
+ATOM 1 X RES 0 0.467 -1.036 0.000 0.14 0.14
+ATOM 2 X RES 1 0.629 0.915 0.000 0.14 0.14
+ATOM 3 X RES 2 0.035 -0.023 0.000 0.14 0.14
+ATOM 4 X RES 3 1.134 -0.192 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.534 1.083 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.677 -0.897 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.053 0.150 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0265 mds.2=-0.0033
+ATOM 1 X RES 0 0.457 -1.031 0.000 0.14 0.14
+ATOM 2 X RES 1 0.661 0.884 0.000 0.14 0.14
+ATOM 3 X RES 2 0.019 -0.022 0.000 0.14 0.14
+ATOM 4 X RES 3 1.093 -0.170 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.526 1.091 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.657 -0.856 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.048 0.105 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0433 mds.2=-0.0053
+ATOM 1 X RES 0 0.445 -1.042 0.000 0.14 0.14
+ATOM 2 X RES 1 0.686 0.856 0.000 0.14 0.14
+ATOM 3 X RES 2 0.000 -0.003 0.000 0.14 0.14
+ATOM 4 X RES 3 1.072 -0.134 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.504 1.092 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.629 -0.849 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.069 0.079 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0514 mds.2=-0.0019
+ATOM 1 X RES 0 0.446 -1.057 0.000 0.14 0.14
+ATOM 2 X RES 1 0.690 0.842 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.014 0.039 0.000 0.14 0.14
+ATOM 4 X RES 3 1.061 -0.115 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.476 1.091 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.599 -0.881 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.108 0.081 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0222 mds.2=0.0031
+ATOM 1 X RES 0 0.460 -1.071 0.000 0.14 0.14
+ATOM 2 X RES 1 0.689 0.864 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.029 0.070 0.000 0.14 0.14
+ATOM 4 X RES 3 1.069 -0.127 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.448 1.080 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.589 -0.913 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.151 0.096 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0129 mds.2=0.0061
+ATOM 1 X RES 0 0.483 -1.079 0.000 0.14 0.14
+ATOM 2 X RES 1 0.694 0.899 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.051 0.079 0.000 0.14 0.14
+ATOM 4 X RES 3 1.075 -0.154 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.426 1.076 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.591 -0.936 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.183 0.114 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0322 mds.2=0.0084
+ATOM 1 X RES 0 0.504 -1.088 0.000 0.14 0.14
+ATOM 2 X RES 1 0.694 0.939 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.067 0.069 0.000 0.14 0.14
+ATOM 4 X RES 3 1.083 -0.178 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.414 1.076 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.598 -0.948 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.202 0.130 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0355 mds.2=0.0080
+ATOM 1 X RES 0 0.521 -1.104 0.000 0.14 0.14
+ATOM 2 X RES 1 0.689 0.969 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.070 0.044 0.000 0.14 0.14
+ATOM 4 X RES 3 1.086 -0.186 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.416 1.078 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.599 -0.948 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.212 0.147 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0337 mds.2=0.0067
+ATOM 1 X RES 0 0.528 -1.126 0.000 0.14 0.14
+ATOM 2 X RES 1 0.674 0.978 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.062 0.017 0.000 0.14 0.14
+ATOM 4 X RES 3 1.087 -0.176 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.414 1.083 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.602 -0.937 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.212 0.161 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0308 mds.2=0.0047
+ATOM 1 X RES 0 0.526 -1.146 0.000 0.14 0.14
+ATOM 2 X RES 1 0.663 0.980 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.043 -0.006 0.000 0.14 0.14
+ATOM 4 X RES 3 1.078 -0.157 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.418 1.081 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.604 -0.928 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.202 0.176 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0253 mds.2=0.0016
+ATOM 1 X RES 0 0.515 -1.157 0.000 0.14 0.14
+ATOM 2 X RES 1 0.662 0.971 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.022 -0.016 0.000 0.14 0.14
+ATOM 4 X RES 3 1.052 -0.136 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.423 1.073 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.605 -0.926 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.179 0.190 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0132 mds.2=-0.0021
+ATOM 1 X RES 0 0.500 -1.156 0.000 0.14 0.14
+ATOM 2 X RES 1 0.662 0.950 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.009 -0.009 0.000 0.14 0.14
+ATOM 4 X RES 3 1.026 -0.109 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.430 1.060 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.601 -0.929 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.149 0.194 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0040 mds.2=-0.0031
+ATOM 1 X RES 0 0.490 -1.141 0.000 0.14 0.14
+ATOM 2 X RES 1 0.667 0.923 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.018 0.011 0.000 0.14 0.14
+ATOM 4 X RES 3 1.026 -0.090 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.440 1.041 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.605 -0.929 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.120 0.184 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0107 mds.2=0.0011
+ATOM 1 X RES 0 0.482 -1.113 0.000 0.14 0.14
+ATOM 2 X RES 1 0.664 0.911 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.041 0.030 0.000 0.14 0.14
+ATOM 4 X RES 3 1.057 -0.086 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.449 1.021 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.614 -0.924 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.099 0.160 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0299 mds.2=0.0060
+ATOM 1 X RES 0 0.469 -1.073 0.000 0.14 0.14
+ATOM 2 X RES 1 0.664 0.908 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.046 0.032 0.000 0.14 0.14
+ATOM 4 X RES 3 1.088 -0.099 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.452 1.016 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.623 -0.918 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.100 0.133 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0540 mds.2=0.0070
+ATOM 1 X RES 0 0.462 -1.031 0.000 0.14 0.14
+ATOM 2 X RES 1 0.667 0.908 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.033 0.032 0.000 0.14 0.14
+ATOM 4 X RES 3 1.115 -0.126 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.459 1.027 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.636 -0.914 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.116 0.105 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0650 mds.2=0.0039
+ATOM 1 X RES 0 0.459 -0.990 0.000 0.14 0.14
+ATOM 2 X RES 1 0.670 0.909 0.000 0.14 0.14
+ATOM 3 X RES 2 0.001 0.022 0.000 0.14 0.14
+ATOM 4 X RES 3 1.147 -0.155 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.481 1.041 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.660 -0.908 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.137 0.082 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0415 mds.2=0.0025
+ATOM 1 X RES 0 0.458 -0.958 0.000 0.14 0.14
+ATOM 2 X RES 1 0.673 0.914 0.000 0.14 0.14
+ATOM 3 X RES 2 0.030 0.011 0.000 0.14 0.14
+ATOM 4 X RES 3 1.180 -0.173 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.501 1.034 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.682 -0.900 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.158 0.072 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0074 mds.2=0.0033
+ATOM 1 X RES 0 0.452 -0.948 0.000 0.14 0.14
+ATOM 2 X RES 1 0.691 0.916 0.000 0.14 0.14
+ATOM 3 X RES 2 0.041 0.013 0.000 0.14 0.14
+ATOM 4 X RES 3 1.215 -0.176 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.519 1.022 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.697 -0.898 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.183 0.071 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0185 mds.2=0.0059
+ATOM 1 X RES 0 0.446 -0.962 0.000 0.14 0.14
+ATOM 2 X RES 1 0.713 0.910 0.000 0.14 0.14
+ATOM 3 X RES 2 0.038 0.039 0.000 0.14 0.14
+ATOM 4 X RES 3 1.246 -0.169 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.542 1.003 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.703 -0.896 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.199 0.075 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0413 mds.2=0.0073
+ATOM 1 X RES 0 0.444 -0.980 0.000 0.14 0.14
+ATOM 2 X RES 1 0.731 0.899 0.000 0.14 0.14
+ATOM 3 X RES 2 0.022 0.062 0.000 0.14 0.14
+ATOM 4 X RES 3 1.271 -0.152 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.562 0.982 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.698 -0.894 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.208 0.083 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0548 mds.2=0.0074
+ATOM 1 X RES 0 0.449 -0.985 0.000 0.14 0.14
+ATOM 2 X RES 1 0.744 0.876 0.000 0.14 0.14
+ATOM 3 X RES 2 0.010 0.066 0.000 0.14 0.14
+ATOM 4 X RES 3 1.287 -0.132 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.584 0.974 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.681 -0.888 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.224 0.090 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0385 mds.2=0.0041
+ATOM 1 X RES 0 0.457 -0.978 0.000 0.14 0.14
+ATOM 2 X RES 1 0.749 0.860 0.000 0.14 0.14
+ATOM 3 X RES 2 0.004 0.048 0.000 0.14 0.14
+ATOM 4 X RES 3 1.284 -0.113 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.602 0.974 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.654 -0.885 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.238 0.095 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0383 mds.2=-0.0006
+ATOM 1 X RES 0 0.468 -0.968 0.000 0.14 0.14
+ATOM 2 X RES 1 0.751 0.850 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.011 0.016 0.000 0.14 0.14
+ATOM 4 X RES 3 1.277 -0.096 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.608 0.977 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.622 -0.872 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.255 0.093 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0584 mds.2=-0.0008
+ATOM 1 X RES 0 0.495 -0.955 0.000 0.14 0.14
+ATOM 2 X RES 1 0.747 0.850 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.021 -0.001 0.000 0.14 0.14
+ATOM 4 X RES 3 1.266 -0.089 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.608 0.980 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.607 -0.862 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.273 0.078 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0584 mds.2=0.0023
+ATOM 1 X RES 0 0.524 -0.942 0.000 0.14 0.14
+ATOM 2 X RES 1 0.740 0.852 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.016 0.013 0.000 0.14 0.14
+ATOM 4 X RES 3 1.257 -0.101 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.607 0.969 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.619 -0.857 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.278 0.066 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0553 mds.2=0.0090
+ATOM 1 X RES 0 0.554 -0.932 0.000 0.14 0.14
+ATOM 2 X RES 1 0.725 0.851 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.009 0.041 0.000 0.14 0.14
+ATOM 4 X RES 3 1.252 -0.114 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.604 0.954 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.647 -0.858 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.271 0.059 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0772 mds.2=0.0146
+ATOM 1 X RES 0 0.575 -0.926 0.000 0.14 0.14
+ATOM 2 X RES 1 0.704 0.850 0.000 0.14 0.14
+ATOM 3 X RES 2 0.001 0.062 0.000 0.14 0.14
+ATOM 4 X RES 3 1.255 -0.119 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.595 0.941 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.668 -0.865 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.272 0.057 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0757 mds.2=0.0157
+ATOM 1 X RES 0 0.592 -0.932 0.000 0.14 0.14
+ATOM 2 X RES 1 0.688 0.864 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.003 0.052 0.000 0.14 0.14
+ATOM 4 X RES 3 1.268 -0.113 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.595 0.943 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.681 -0.874 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.270 0.061 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0644 mds.2=0.0144
+ATOM 1 X RES 0 0.599 -0.943 0.000 0.14 0.14
+ATOM 2 X RES 1 0.672 0.883 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.009 0.013 0.000 0.14 0.14
+ATOM 4 X RES 3 1.284 -0.097 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.596 0.954 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.687 -0.880 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.264 0.069 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0816 mds.2=0.0141
+ATOM 1 X RES 0 0.594 -0.950 0.000 0.14 0.14
+ATOM 2 X RES 1 0.649 0.894 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.016 -0.032 0.000 0.14 0.14
+ATOM 4 X RES 3 1.298 -0.075 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.590 0.976 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.680 -0.887 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.255 0.075 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.1045 mds.2=0.0148
+ATOM 1 X RES 0 0.584 -0.961 0.000 0.14 0.14
+ATOM 2 X RES 1 0.625 0.904 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.018 -0.067 0.000 0.14 0.14
+ATOM 4 X RES 3 1.301 -0.049 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.570 0.992 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.676 -0.911 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.246 0.091 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0867 mds.2=0.0111
+ATOM 1 X RES 0 0.570 -0.975 0.000 0.14 0.14
+ATOM 2 X RES 1 0.593 0.918 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.012 -0.079 0.000 0.14 0.14
+ATOM 4 X RES 3 1.293 -0.031 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.541 1.000 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.676 -0.943 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.226 0.110 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0365 mds.2=0.0014
+ATOM 1 X RES 0 0.566 -0.989 0.000 0.14 0.14
+ATOM 2 X RES 1 0.557 0.929 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.014 -0.063 0.000 0.14 0.14
+ATOM 4 X RES 3 1.280 -0.026 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.512 1.000 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.676 -0.975 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.201 0.123 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0113 mds.2=-0.0067
+ATOM 1 X RES 0 0.560 -1.007 0.000 0.14 0.14
+ATOM 2 X RES 1 0.538 0.934 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.024 -0.035 0.000 0.14 0.14
+ATOM 4 X RES 3 1.247 -0.023 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.484 0.999 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.666 -1.000 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.171 0.132 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0272 mds.2=-0.0074
+ATOM 1 X RES 0 0.548 -1.019 0.000 0.14 0.14
+ATOM 2 X RES 1 0.557 0.932 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.041 -0.008 0.000 0.14 0.14
+ATOM 4 X RES 3 1.199 -0.021 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.477 0.998 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.648 -1.020 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.138 0.138 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0381 mds.2=-0.0012
+ATOM 1 X RES 0 0.528 -1.023 0.000 0.14 0.14
+ATOM 2 X RES 1 0.606 0.928 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.052 0.007 0.000 0.14 0.14
+ATOM 4 X RES 3 1.141 -0.021 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.490 1.005 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.623 -1.029 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.110 0.133 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0548 mds.2=0.0021
+ATOM 1 X RES 0 0.511 -1.021 0.000 0.14 0.14
+ATOM 2 X RES 1 0.637 0.924 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.048 0.009 0.000 0.14 0.14
+ATOM 4 X RES 3 1.078 -0.023 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.493 1.027 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.588 -1.026 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.098 0.111 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0470 mds.2=0.0012
+ATOM 1 X RES 0 0.498 -1.018 0.000 0.14 0.14
+ATOM 2 X RES 1 0.646 0.938 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.027 0.002 0.000 0.14 0.14
+ATOM 4 X RES 3 1.025 -0.046 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.486 1.055 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.564 -1.011 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.092 0.080 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0227 mds.2=-0.0019
+ATOM 1 X RES 0 0.484 -1.020 0.000 0.14 0.14
+ATOM 2 X RES 1 0.655 0.970 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.014 -0.007 0.000 0.14 0.14
+ATOM 4 X RES 3 1.002 -0.086 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.478 1.071 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.555 -0.984 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.094 0.057 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0132 mds.2=-0.0022
+ATOM 1 X RES 0 0.483 -1.040 0.000 0.14 0.14
+ATOM 2 X RES 1 0.663 1.007 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.025 -0.006 0.000 0.14 0.14
+ATOM 4 X RES 3 1.020 -0.112 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.465 1.076 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.579 -0.959 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.096 0.033 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0040 mds.2=0.0004
+ATOM 1 X RES 0 0.492 -1.073 0.000 0.14 0.14
+ATOM 2 X RES 1 0.663 1.040 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.040 0.005 0.000 0.14 0.14
+ATOM 4 X RES 3 1.058 -0.126 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.452 1.063 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.622 -0.934 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.099 0.024 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0045 mds.2=0.0008
+ATOM 1 X RES 0 0.499 -1.096 0.000 0.14 0.14
+ATOM 2 X RES 1 0.654 1.060 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.040 0.026 0.000 0.14 0.14
+ATOM 4 X RES 3 1.098 -0.131 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.439 1.035 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.658 -0.925 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.114 0.030 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0145 mds.2=0.0006
+ATOM 1 X RES 0 0.502 -1.105 0.000 0.14 0.14
+ATOM 2 X RES 1 0.649 1.059 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.026 0.043 0.000 0.14 0.14
+ATOM 4 X RES 3 1.136 -0.132 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.444 1.013 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.681 -0.930 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.137 0.052 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0116 mds.2=0.0025
+ATOM 1 X RES 0 0.491 -1.106 0.000 0.14 0.14
+ATOM 2 X RES 1 0.655 1.046 0.000 0.14 0.14
+ATOM 3 X RES 2 0.004 0.040 0.000 0.14 0.14
+ATOM 4 X RES 3 1.157 -0.125 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.454 0.999 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.696 -0.942 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.156 0.089 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0031 mds.2=0.0044
+ATOM 1 X RES 0 0.471 -1.102 0.000 0.14 0.14
+ATOM 2 X RES 1 0.654 1.027 0.000 0.14 0.14
+ATOM 3 X RES 2 0.043 0.017 0.000 0.14 0.14
+ATOM 4 X RES 3 1.167 -0.106 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.460 0.990 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.713 -0.950 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.162 0.124 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0148 mds.2=0.0086
+ATOM 1 X RES 0 0.446 -1.081 0.000 0.14 0.14
+ATOM 2 X RES 1 0.656 1.001 0.000 0.14 0.14
+ATOM 3 X RES 2 0.075 -0.013 0.000 0.14 0.14
+ATOM 4 X RES 3 1.176 -0.089 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.469 0.991 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.722 -0.960 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.161 0.151 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0318 mds.2=0.0109
+ATOM 1 X RES 0 0.417 -1.048 0.000 0.14 0.14
+ATOM 2 X RES 1 0.661 0.966 0.000 0.14 0.14
+ATOM 3 X RES 2 0.090 -0.029 0.000 0.14 0.14
+ATOM 4 X RES 3 1.186 -0.077 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.476 0.993 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.716 -0.969 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.163 0.163 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0166 mds.2=0.0078
+ATOM 1 X RES 0 0.398 -1.020 0.000 0.14 0.14
+ATOM 2 X RES 1 0.662 0.922 0.000 0.14 0.14
+ATOM 3 X RES 2 0.082 -0.029 0.000 0.14 0.14
+ATOM 4 X RES 3 1.199 -0.071 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.474 1.000 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.706 -0.970 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.159 0.168 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0154 mds.2=0.0036
+ATOM 1 X RES 0 0.390 -1.013 0.000 0.14 0.14
+ATOM 2 X RES 1 0.659 0.885 0.000 0.14 0.14
+ATOM 3 X RES 2 0.059 -0.009 0.000 0.14 0.14
+ATOM 4 X RES 3 1.204 -0.080 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.463 1.011 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.702 -0.957 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.147 0.163 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0451 mds.2=0.0018
+ATOM 1 X RES 0 0.390 -1.025 0.000 0.14 0.14
+ATOM 2 X RES 1 0.669 0.857 0.000 0.14 0.14
+ATOM 3 X RES 2 0.017 0.021 0.000 0.14 0.14
+ATOM 4 X RES 3 1.198 -0.102 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.453 1.026 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.695 -0.925 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.127 0.149 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0364 mds.2=0.0021
+ATOM 1 X RES 0 0.396 -1.038 0.000 0.14 0.14
+ATOM 2 X RES 1 0.685 0.851 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.027 0.030 0.000 0.14 0.14
+ATOM 4 X RES 3 1.187 -0.126 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.443 1.042 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.696 -0.890 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.103 0.131 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0125 mds.2=0.0036
+ATOM 1 X RES 0 0.401 -1.038 0.000 0.14 0.14
+ATOM 2 X RES 1 0.706 0.851 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.057 0.024 0.000 0.14 0.14
+ATOM 4 X RES 3 1.178 -0.153 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.432 1.057 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.707 -0.861 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.088 0.120 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0330 mds.2=0.0045
+ATOM 1 X RES 0 0.402 -1.032 0.000 0.14 0.14
+ATOM 2 X RES 1 0.718 0.845 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.048 0.014 0.000 0.14 0.14
+ATOM 4 X RES 3 1.164 -0.182 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.420 1.069 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.717 -0.850 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.100 0.136 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0605 mds.2=0.0048
+ATOM 1 X RES 0 0.401 -1.026 0.000 0.14 0.14
+ATOM 2 X RES 1 0.725 0.834 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.010 0.009 0.000 0.14 0.14
+ATOM 4 X RES 3 1.148 -0.199 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.410 1.072 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.723 -0.858 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.131 0.167 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0417 mds.2=0.0041
+ATOM 1 X RES 0 0.400 -1.027 0.000 0.14 0.14
+ATOM 2 X RES 1 0.733 0.830 0.000 0.14 0.14
+ATOM 3 X RES 2 0.029 -0.003 0.000 0.14 0.14
+ATOM 4 X RES 3 1.130 -0.204 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.397 1.067 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.733 -0.870 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.162 0.207 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0115 mds.2=0.0011
+ATOM 1 X RES 0 0.390 -1.042 0.000 0.14 0.14
+ATOM 2 X RES 1 0.736 0.829 0.000 0.14 0.14
+ATOM 3 X RES 2 0.048 -0.020 0.000 0.14 0.14
+ATOM 4 X RES 3 1.109 -0.206 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.370 1.060 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.736 -0.871 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.178 0.250 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0257 mds.2=-0.0018
+ATOM 1 X RES 0 0.376 -1.072 0.000 0.14 0.14
+ATOM 2 X RES 1 0.742 0.834 0.000 0.14 0.14
+ATOM 3 X RES 2 0.033 -0.029 0.000 0.14 0.14
+ATOM 4 X RES 3 1.098 -0.199 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.341 1.042 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.732 -0.863 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.177 0.288 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0451 mds.2=-0.0029
+ATOM 1 X RES 0 0.362 -1.103 0.000 0.14 0.14
+ATOM 2 X RES 1 0.751 0.849 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.002 -0.034 0.000 0.14 0.14
+ATOM 4 X RES 3 1.096 -0.197 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.314 1.028 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.728 -0.858 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.166 0.315 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0387 mds.2=-0.0032
+ATOM 1 X RES 0 0.351 -1.127 0.000 0.14 0.14
+ATOM 2 X RES 1 0.755 0.868 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.028 -0.032 0.000 0.14 0.14
+ATOM 4 X RES 3 1.091 -0.206 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.295 1.015 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.723 -0.850 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.152 0.332 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0254 mds.2=-0.0017
+ATOM 1 X RES 0 0.350 -1.138 0.000 0.14 0.14
+ATOM 2 X RES 1 0.762 0.876 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.040 -0.033 0.000 0.14 0.14
+ATOM 4 X RES 3 1.082 -0.218 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.289 1.017 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.722 -0.842 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.141 0.337 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0311 mds.2=-0.0001
+ATOM 1 X RES 0 0.348 -1.137 0.000 0.14 0.14
+ATOM 2 X RES 1 0.773 0.863 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.033 -0.034 0.000 0.14 0.14
+ATOM 4 X RES 3 1.069 -0.221 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.296 1.033 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.728 -0.838 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.134 0.334 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0448 mds.2=0.0006
+ATOM 1 X RES 0 0.349 -1.130 0.000 0.14 0.14
+ATOM 2 X RES 1 0.786 0.848 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.018 -0.026 0.000 0.14 0.14
+ATOM 4 X RES 3 1.055 -0.219 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.306 1.052 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.740 -0.847 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.126 0.321 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0499 mds.2=0.0020
+ATOM 1 X RES 0 0.348 -1.114 0.000 0.14 0.14
+ATOM 2 X RES 1 0.803 0.839 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.010 -0.015 0.000 0.14 0.14
+ATOM 4 X RES 3 1.036 -0.230 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.313 1.076 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.753 -0.853 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.111 0.297 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0543 mds.2=0.0037
+ATOM 1 X RES 0 0.346 -1.099 0.000 0.14 0.14
+ATOM 2 X RES 1 0.807 0.831 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.022 -0.000 0.000 0.14 0.14
+ATOM 4 X RES 3 1.035 -0.245 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.307 1.101 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.765 -0.851 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.094 0.263 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0486 mds.2=0.0054
+ATOM 1 X RES 0 0.340 -1.088 0.000 0.14 0.14
+ATOM 2 X RES 1 0.800 0.820 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.045 0.014 0.000 0.14 0.14
+ATOM 4 X RES 3 1.044 -0.258 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.291 1.124 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.772 -0.842 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.076 0.230 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0459 mds.2=0.0051
+ATOM 1 X RES 0 0.324 -1.076 0.000 0.14 0.14
+ATOM 2 X RES 1 0.794 0.807 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.056 0.023 0.000 0.14 0.14
+ATOM 4 X RES 3 1.057 -0.265 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.273 1.140 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.774 -0.833 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.072 0.204 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0715 mds.2=-0.0001
+ATOM 1 X RES 0 0.302 -1.065 0.000 0.14 0.14
+ATOM 2 X RES 1 0.791 0.796 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.032 0.033 0.000 0.14 0.14
+ATOM 4 X RES 3 1.075 -0.274 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.258 1.147 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.771 -0.829 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.107 0.191 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0764 mds.2=-0.0063
+ATOM 1 X RES 0 0.282 -1.051 0.000 0.14 0.14
+ATOM 2 X RES 1 0.789 0.786 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.006 0.037 0.000 0.14 0.14
+ATOM 4 X RES 3 1.105 -0.276 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.245 1.145 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.774 -0.830 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.150 0.188 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0603 mds.2=-0.0119
+ATOM 1 X RES 0 0.269 -1.042 0.000 0.14 0.14
+ATOM 2 X RES 1 0.786 0.780 0.000 0.14 0.14
+ATOM 3 X RES 2 0.013 0.029 0.000 0.14 0.14
+ATOM 4 X RES 3 1.122 -0.278 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.236 1.140 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.772 -0.834 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.182 0.205 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0378 mds.2=-0.0153
+ATOM 1 X RES 0 0.282 -1.040 0.000 0.14 0.14
+ATOM 2 X RES 1 0.795 0.780 0.000 0.14 0.14
+ATOM 3 X RES 2 0.013 0.022 0.000 0.14 0.14
+ATOM 4 X RES 3 1.131 -0.283 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.242 1.132 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.765 -0.842 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.214 0.232 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0214 mds.2=-0.0124
+ATOM 1 X RES 0 0.310 -1.045 0.000 0.14 0.14
+ATOM 2 X RES 1 0.811 0.797 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.003 0.019 0.000 0.14 0.14
+ATOM 4 X RES 3 1.135 -0.296 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.256 1.117 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.762 -0.850 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.236 0.258 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0063 mds.2=-0.0091
+ATOM 1 X RES 0 0.338 -1.045 0.000 0.14 0.14
+ATOM 2 X RES 1 0.827 0.812 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.017 0.015 0.000 0.14 0.14
+ATOM 4 X RES 3 1.134 -0.303 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.275 1.102 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.759 -0.858 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.249 0.277 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0095 mds.2=-0.0016
+ATOM 1 X RES 0 0.359 -1.042 0.000 0.14 0.14
+ATOM 2 X RES 1 0.839 0.831 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.036 0.006 0.000 0.14 0.14
+ATOM 4 X RES 3 1.145 -0.304 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.302 1.079 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.757 -0.862 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.247 0.293 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0259 mds.2=0.0036
+ATOM 1 X RES 0 0.364 -1.045 0.000 0.14 0.14
+ATOM 2 X RES 1 0.840 0.847 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.042 -0.007 0.000 0.14 0.14
+ATOM 4 X RES 3 1.166 -0.285 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.331 1.047 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.761 -0.865 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.236 0.307 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0234 mds.2=0.0061
+ATOM 1 X RES 0 0.357 -1.055 0.000 0.14 0.14
+ATOM 2 X RES 1 0.838 0.857 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.034 -0.016 0.000 0.14 0.14
+ATOM 4 X RES 3 1.182 -0.257 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.359 1.016 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.771 -0.854 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.213 0.309 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 5.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0012 mds.2=0.0060
+ATOM 1 X RES 0 0.353 -1.075 0.000 0.14 0.14
+ATOM 2 X RES 1 0.832 0.857 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.020 -0.029 0.000 0.14 0.14
+ATOM 4 X RES 3 1.183 -0.223 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.384 0.999 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.786 -0.831 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.178 0.303 0.000 0.14 0.14
+END
diff --git a/regtest/dimred/rt-mds2/analysis.0.list_embed.reference b/regtest/dimred/rt-mds2/analysis.0.list_embed.reference
new file mode 100644
index 000000000..185b19ed5
--- /dev/null
+++ b/regtest/dimred/rt-mds2/analysis.0.list_embed.reference
@@ -0,0 +1,101 @@
+#! FIELDS mds.1 mds.2
+ 0.0873 0.0013
+ 0.0535 0.0044
+ 0.0150 0.0044
+ -0.0136 0.0019
+ -0.0308 -0.0012
+ -0.0355 -0.0018
+ -0.0090 -0.0015
+ 0.0145 0.0004
+ 0.0191 0.0022
+ 0.0278 0.0015
+ 0.0091 -0.0004
+ -0.0359 -0.0012
+ -0.0540 0.0004
+ -0.0322 -0.0034
+ -0.0205 -0.0150
+ -0.0282 -0.0289
+ -0.0530 -0.0358
+ -0.0769 -0.0312
+ -0.0893 -0.0259
+ -0.0697 -0.0246
+ -0.0302 -0.0196
+ 0.0093 -0.0072
+ 0.0274 0.0009
+ 0.0301 0.0016
+ 0.0265 -0.0033
+ 0.0433 -0.0053
+ 0.0514 -0.0019
+ 0.0222 0.0031
+ -0.0129 0.0061
+ -0.0322 0.0084
+ -0.0355 0.0080
+ -0.0337 0.0067
+ -0.0308 0.0047
+ -0.0253 0.0016
+ -0.0132 -0.0021
+ 0.0040 -0.0031
+ 0.0107 0.0011
+ 0.0299 0.0060
+ 0.0540 0.0070
+ 0.0650 0.0039
+ 0.0415 0.0025
+ 0.0074 0.0033
+ -0.0185 0.0059
+ -0.0413 0.0073
+ -0.0548 0.0074
+ -0.0385 0.0041
+ -0.0383 -0.0006
+ -0.0584 -0.0008
+ -0.0584 0.0023
+ -0.0553 0.0090
+ -0.0772 0.0146
+ -0.0757 0.0157
+ -0.0644 0.0144
+ -0.0816 0.0141
+ -0.1045 0.0148
+ -0.0867 0.0111
+ -0.0365 0.0014
+ 0.0113 -0.0067
+ 0.0272 -0.0074
+ 0.0381 -0.0012
+ 0.0548 0.0021
+ 0.0470 0.0012
+ 0.0227 -0.0019
+ 0.0132 -0.0022
+ 0.0040 0.0004
+ -0.0045 0.0008
+ -0.0145 0.0006
+ -0.0116 0.0025
+ -0.0031 0.0044
+ -0.0148 0.0086
+ -0.0318 0.0109
+ -0.0166 0.0078
+ 0.0154 0.0036
+ 0.0451 0.0018
+ 0.0364 0.0021
+ 0.0125 0.0036
+ 0.0330 0.0045
+ 0.0605 0.0048
+ 0.0417 0.0041
+ 0.0115 0.0011
+ 0.0257 -0.0018
+ 0.0451 -0.0029
+ 0.0387 -0.0032
+ 0.0254 -0.0017
+ 0.0311 -0.0001
+ 0.0448 0.0006
+ 0.0499 0.0020
+ 0.0543 0.0037
+ 0.0486 0.0054
+ 0.0459 0.0051
+ 0.0715 -0.0001
+ 0.0764 -0.0063
+ 0.0603 -0.0119
+ 0.0378 -0.0153
+ 0.0214 -0.0124
+ 0.0063 -0.0091
+ -0.0095 -0.0016
+ -0.0259 0.0036
+ -0.0234 0.0061
+ 0.0012 0.0060
diff --git a/regtest/dimred/rt-mds2/config b/regtest/dimred/rt-mds2/config
new file mode 100644
index 000000000..57d886c44
--- /dev/null
+++ b/regtest/dimred/rt-mds2/config
@@ -0,0 +1,2 @@
+type=simplemd
+
diff --git a/regtest/dimred/rt-mds2/embed.reference b/regtest/dimred/rt-mds2/embed.reference
new file mode 100644
index 000000000..0aa75c0e6
--- /dev/null
+++ b/regtest/dimred/rt-mds2/embed.reference
@@ -0,0 +1,1200 @@
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0594 mds.2=0.0053
+ATOM 1 X RES 0 0.349 -1.094 0.000 0.14 0.14
+ATOM 2 X RES 1 0.829 0.855 0.000 0.14 0.14
+ATOM 3 X RES 2 0.002 -0.048 0.000 0.14 0.14
+ATOM 4 X RES 3 1.173 -0.187 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.394 0.997 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.802 -0.808 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.157 0.285 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0683 mds.2=0.0034
+ATOM 1 X RES 0 0.343 -1.113 0.000 0.14 0.14
+ATOM 2 X RES 1 0.812 0.851 0.000 0.14 0.14
+ATOM 3 X RES 2 0.031 -0.064 0.000 0.14 0.14
+ATOM 4 X RES 3 1.156 -0.154 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.381 1.007 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.818 -0.785 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.143 0.258 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0705 mds.2=0.0006
+ATOM 1 X RES 0 0.325 -1.135 0.000 0.14 0.14
+ATOM 2 X RES 1 0.792 0.850 0.000 0.14 0.14
+ATOM 3 X RES 2 0.054 -0.068 0.000 0.14 0.14
+ATOM 4 X RES 3 1.144 -0.137 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.356 1.024 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.828 -0.768 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.132 0.234 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0729 mds.2=-0.0019
+ATOM 1 X RES 0 0.306 -1.145 0.000 0.14 0.14
+ATOM 2 X RES 1 0.766 0.873 0.000 0.14 0.14
+ATOM 3 X RES 2 0.057 -0.066 0.000 0.14 0.14
+ATOM 4 X RES 3 1.135 -0.146 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.322 1.028 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.827 -0.770 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.116 0.227 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0874 mds.2=-0.0069
+ATOM 1 X RES 0 0.289 -1.147 0.000 0.14 0.14
+ATOM 2 X RES 1 0.737 0.907 0.000 0.14 0.14
+ATOM 3 X RES 2 0.043 -0.053 0.000 0.14 0.14
+ATOM 4 X RES 3 1.132 -0.170 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.293 1.022 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.810 -0.796 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.098 0.238 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0961 mds.2=-0.0095
+ATOM 1 X RES 0 0.267 -1.139 0.000 0.14 0.14
+ATOM 2 X RES 1 0.734 0.931 0.000 0.14 0.14
+ATOM 3 X RES 2 0.025 -0.037 0.000 0.14 0.14
+ATOM 4 X RES 3 1.130 -0.202 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.291 1.022 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.794 -0.834 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.071 0.258 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0867 mds.2=-0.0062
+ATOM 1 X RES 0 0.267 -1.128 0.000 0.14 0.14
+ATOM 2 X RES 1 0.755 0.942 0.000 0.14 0.14
+ATOM 3 X RES 2 0.012 -0.028 0.000 0.14 0.14
+ATOM 4 X RES 3 1.114 -0.222 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.320 1.032 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.785 -0.866 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.042 0.270 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0719 mds.2=-0.0008
+ATOM 1 X RES 0 0.283 -1.113 0.000 0.14 0.14
+ATOM 2 X RES 1 0.778 0.943 0.000 0.14 0.14
+ATOM 3 X RES 2 0.009 -0.020 0.000 0.14 0.14
+ATOM 4 X RES 3 1.091 -0.233 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.343 1.052 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.785 -0.889 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.033 0.261 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0575 mds.2=0.0031
+ATOM 1 X RES 0 0.307 -1.095 0.000 0.14 0.14
+ATOM 2 X RES 1 0.800 0.940 0.000 0.14 0.14
+ATOM 3 X RES 2 0.016 -0.004 0.000 0.14 0.14
+ATOM 4 X RES 3 1.067 -0.244 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.351 1.076 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.787 -0.901 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.051 0.228 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0552 mds.2=0.0034
+ATOM 1 X RES 0 0.336 -1.075 0.000 0.14 0.14
+ATOM 2 X RES 1 0.820 0.922 0.000 0.14 0.14
+ATOM 3 X RES 2 0.021 0.018 0.000 0.14 0.14
+ATOM 4 X RES 3 1.044 -0.256 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.356 1.097 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.787 -0.902 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.078 0.196 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0682 mds.2=-0.0002
+ATOM 1 X RES 0 0.356 -1.053 0.000 0.14 0.14
+ATOM 2 X RES 1 0.830 0.890 0.000 0.14 0.14
+ATOM 3 X RES 2 0.009 0.041 0.000 0.14 0.14
+ATOM 4 X RES 3 1.034 -0.261 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.352 1.113 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.780 -0.897 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.097 0.166 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0781 mds.2=-0.0024
+ATOM 1 X RES 0 0.355 -1.042 0.000 0.14 0.14
+ATOM 2 X RES 1 0.832 0.848 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.008 0.067 0.000 0.14 0.14
+ATOM 4 X RES 3 1.038 -0.246 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.343 1.122 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.763 -0.884 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.109 0.135 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0785 mds.2=-0.0025
+ATOM 1 X RES 0 0.344 -1.043 0.000 0.14 0.14
+ATOM 2 X RES 1 0.825 0.811 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.029 0.087 0.000 0.14 0.14
+ATOM 4 X RES 3 1.056 -0.218 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.339 1.127 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.738 -0.873 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.119 0.109 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0763 mds.2=-0.0027
+ATOM 1 X RES 0 0.332 -1.041 0.000 0.14 0.14
+ATOM 2 X RES 1 0.810 0.796 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.041 0.091 0.000 0.14 0.14
+ATOM 4 X RES 3 1.082 -0.211 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.347 1.138 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.715 -0.877 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.120 0.105 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0755 mds.2=-0.0041
+ATOM 1 X RES 0 0.334 -1.037 0.000 0.14 0.14
+ATOM 2 X RES 1 0.778 0.804 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.039 0.080 0.000 0.14 0.14
+ATOM 4 X RES 3 1.109 -0.218 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.355 1.153 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.703 -0.893 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.123 0.110 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0792 mds.2=-0.0069
+ATOM 1 X RES 0 0.355 -1.033 0.000 0.14 0.14
+ATOM 2 X RES 1 0.742 0.821 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.025 0.056 0.000 0.14 0.14
+ATOM 4 X RES 3 1.135 -0.222 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.359 1.164 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.709 -0.907 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.139 0.120 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0778 mds.2=-0.0062
+ATOM 1 X RES 0 0.380 -1.027 0.000 0.14 0.14
+ATOM 2 X RES 1 0.714 0.842 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.018 0.024 0.000 0.14 0.14
+ATOM 4 X RES 3 1.163 -0.220 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.361 1.157 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.716 -0.913 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.162 0.138 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0727 mds.2=-0.0025
+ATOM 1 X RES 0 0.401 -1.023 0.000 0.14 0.14
+ATOM 2 X RES 1 0.698 0.857 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.021 0.001 0.000 0.14 0.14
+ATOM 4 X RES 3 1.182 -0.210 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.368 1.135 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.713 -0.914 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.179 0.153 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0726 mds.2=0.0014
+ATOM 1 X RES 0 0.421 -1.019 0.000 0.14 0.14
+ATOM 2 X RES 1 0.692 0.863 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.019 -0.014 0.000 0.14 0.14
+ATOM 4 X RES 3 1.184 -0.196 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.388 1.097 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.705 -0.908 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.185 0.177 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0756 mds.2=0.0030
+ATOM 1 X RES 0 0.446 -1.017 0.000 0.14 0.14
+ATOM 2 X RES 1 0.685 0.863 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.015 -0.025 0.000 0.14 0.14
+ATOM 4 X RES 3 1.179 -0.185 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.416 1.052 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.696 -0.895 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.182 0.207 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0821 mds.2=0.0017
+ATOM 1 X RES 0 0.457 -1.019 0.000 0.14 0.14
+ATOM 2 X RES 1 0.680 0.855 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.011 -0.026 0.000 0.14 0.14
+ATOM 4 X RES 3 1.179 -0.176 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.442 1.007 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.697 -0.876 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.167 0.235 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0816 mds.2=0.0001
+ATOM 1 X RES 0 0.458 -1.031 0.000 0.14 0.14
+ATOM 2 X RES 1 0.674 0.846 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.012 -0.024 0.000 0.14 0.14
+ATOM 4 X RES 3 1.180 -0.158 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.447 0.975 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.696 -0.857 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.156 0.249 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0774 mds.2=0.0008
+ATOM 1 X RES 0 0.456 -1.043 0.000 0.14 0.14
+ATOM 2 X RES 1 0.671 0.835 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.000 -0.026 0.000 0.14 0.14
+ATOM 4 X RES 3 1.166 -0.143 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.428 0.986 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.698 -0.839 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.167 0.230 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0766 mds.2=0.0008
+ATOM 1 X RES 0 0.452 -1.055 0.000 0.14 0.14
+ATOM 2 X RES 1 0.677 0.828 0.000 0.14 0.14
+ATOM 3 X RES 2 0.006 -0.027 0.000 0.14 0.14
+ATOM 4 X RES 3 1.151 -0.129 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.409 1.009 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.699 -0.822 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.178 0.197 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0838 mds.2=-0.0005
+ATOM 1 X RES 0 0.446 -1.054 0.000 0.14 0.14
+ATOM 2 X RES 1 0.680 0.828 0.000 0.14 0.14
+ATOM 3 X RES 2 0.012 -0.019 0.000 0.14 0.14
+ATOM 4 X RES 3 1.144 -0.134 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.397 1.033 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.703 -0.818 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.182 0.164 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0931 mds.2=-0.0016
+ATOM 1 X RES 0 0.438 -1.056 0.000 0.14 0.14
+ATOM 2 X RES 1 0.688 0.834 0.000 0.14 0.14
+ATOM 3 X RES 2 0.009 -0.007 0.000 0.14 0.14
+ATOM 4 X RES 3 1.142 -0.157 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.393 1.057 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.706 -0.822 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.178 0.151 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0936 mds.2=-0.0010
+ATOM 1 X RES 0 0.428 -1.045 0.000 0.14 0.14
+ATOM 2 X RES 1 0.699 0.841 0.000 0.14 0.14
+ATOM 3 X RES 2 0.001 0.007 0.000 0.14 0.14
+ATOM 4 X RES 3 1.148 -0.194 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.389 1.073 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.707 -0.840 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.180 0.158 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0923 mds.2=-0.0009
+ATOM 1 X RES 0 0.403 -1.025 0.000 0.14 0.14
+ATOM 2 X RES 1 0.715 0.853 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.004 0.012 0.000 0.14 0.14
+ATOM 4 X RES 3 1.155 -0.230 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.392 1.085 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.705 -0.866 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.171 0.170 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0906 mds.2=-0.0008
+ATOM 1 X RES 0 0.386 -1.012 0.000 0.14 0.14
+ATOM 2 X RES 1 0.732 0.863 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.022 0.014 0.000 0.14 0.14
+ATOM 4 X RES 3 1.156 -0.250 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.397 1.085 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.714 -0.879 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.142 0.179 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0706 mds.2=0.0025
+ATOM 1 X RES 0 0.373 -1.014 0.000 0.14 0.14
+ATOM 2 X RES 1 0.748 0.860 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.046 0.020 0.000 0.14 0.14
+ATOM 4 X RES 3 1.155 -0.251 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.403 1.078 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.723 -0.884 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.104 0.192 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0664 mds.2=0.0050
+ATOM 1 X RES 0 0.366 -1.022 0.000 0.14 0.14
+ATOM 2 X RES 1 0.759 0.848 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.053 0.026 0.000 0.14 0.14
+ATOM 4 X RES 3 1.139 -0.236 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.395 1.066 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.739 -0.888 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.078 0.207 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0901 mds.2=0.0019
+ATOM 1 X RES 0 0.361 -1.036 0.000 0.14 0.14
+ATOM 2 X RES 1 0.763 0.828 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.033 0.026 0.000 0.14 0.14
+ATOM 4 X RES 3 1.121 -0.214 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.380 1.056 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.754 -0.879 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.078 0.218 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.1059 mds.2=-0.0015
+ATOM 1 X RES 0 0.352 -1.047 0.000 0.14 0.14
+ATOM 2 X RES 1 0.756 0.807 0.000 0.14 0.14
+ATOM 3 X RES 2 0.006 0.013 0.000 0.14 0.14
+ATOM 4 X RES 3 1.104 -0.192 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.359 1.052 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.768 -0.859 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.090 0.226 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0917 mds.2=0.0006
+ATOM 1 X RES 0 0.344 -1.045 0.000 0.14 0.14
+ATOM 2 X RES 1 0.741 0.800 0.000 0.14 0.14
+ATOM 3 X RES 2 0.035 -0.004 0.000 0.14 0.14
+ATOM 4 X RES 3 1.096 -0.186 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.335 1.047 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.779 -0.842 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.101 0.231 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0876 mds.2=0.0021
+ATOM 1 X RES 0 0.337 -1.041 0.000 0.14 0.14
+ATOM 2 X RES 1 0.721 0.814 0.000 0.14 0.14
+ATOM 3 X RES 2 0.037 -0.029 0.000 0.14 0.14
+ATOM 4 X RES 3 1.104 -0.208 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.311 1.042 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.787 -0.822 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.103 0.244 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.1008 mds.2=-0.0001
+ATOM 1 X RES 0 0.347 -1.053 0.000 0.14 0.14
+ATOM 2 X RES 1 0.715 0.841 0.000 0.14 0.14
+ATOM 3 X RES 2 0.007 -0.046 0.000 0.14 0.14
+ATOM 4 X RES 3 1.122 -0.236 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.304 1.039 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.787 -0.808 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.100 0.262 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0955 mds.2=-0.0014
+ATOM 1 X RES 0 0.356 -1.078 0.000 0.14 0.14
+ATOM 2 X RES 1 0.732 0.861 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.018 -0.040 0.000 0.14 0.14
+ATOM 4 X RES 3 1.137 -0.254 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.323 1.034 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.788 -0.804 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.097 0.282 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0858 mds.2=-0.0018
+ATOM 1 X RES 0 0.357 -1.092 0.000 0.14 0.14
+ATOM 2 X RES 1 0.756 0.865 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.028 -0.023 0.000 0.14 0.14
+ATOM 4 X RES 3 1.144 -0.264 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.339 1.030 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.794 -0.797 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.097 0.282 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0894 mds.2=-0.0005
+ATOM 1 X RES 0 0.358 -1.096 0.000 0.14 0.14
+ATOM 2 X RES 1 0.777 0.847 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.021 -0.007 0.000 0.14 0.14
+ATOM 4 X RES 3 1.139 -0.268 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.344 1.036 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.796 -0.790 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.113 0.279 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0922 mds.2=0.0014
+ATOM 1 X RES 0 0.351 -1.091 0.000 0.14 0.14
+ATOM 2 X RES 1 0.792 0.830 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.010 0.005 0.000 0.14 0.14
+ATOM 4 X RES 3 1.128 -0.274 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.342 1.049 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.780 -0.792 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.139 0.272 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0917 mds.2=0.0010
+ATOM 1 X RES 0 0.344 -1.081 0.000 0.14 0.14
+ATOM 2 X RES 1 0.795 0.799 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.003 0.015 0.000 0.14 0.14
+ATOM 4 X RES 3 1.112 -0.267 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.331 1.063 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.755 -0.798 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.161 0.269 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0925 mds.2=-0.0043
+ATOM 1 X RES 0 0.337 -1.065 0.000 0.14 0.14
+ATOM 2 X RES 1 0.791 0.762 0.000 0.14 0.14
+ATOM 3 X RES 2 0.001 0.019 0.000 0.14 0.14
+ATOM 4 X RES 3 1.094 -0.251 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.316 1.086 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.733 -0.814 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.173 0.262 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0967 mds.2=-0.0102
+ATOM 1 X RES 0 0.332 -1.048 0.000 0.14 0.14
+ATOM 2 X RES 1 0.784 0.753 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.005 0.021 0.000 0.14 0.14
+ATOM 4 X RES 3 1.083 -0.247 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.297 1.102 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.723 -0.828 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.174 0.247 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.1073 mds.2=-0.0096
+ATOM 1 X RES 0 0.335 -1.045 0.000 0.14 0.14
+ATOM 2 X RES 1 0.777 0.781 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.026 0.013 0.000 0.14 0.14
+ATOM 4 X RES 3 1.083 -0.259 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.285 1.111 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.723 -0.832 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.161 0.231 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.1065 mds.2=-0.0047
+ATOM 1 X RES 0 0.345 -1.053 0.000 0.14 0.14
+ATOM 2 X RES 1 0.770 0.830 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.045 0.000 0.000 0.14 0.14
+ATOM 4 X RES 3 1.085 -0.267 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.274 1.114 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.737 -0.835 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.143 0.211 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0935 mds.2=-0.0003
+ATOM 1 X RES 0 0.359 -1.063 0.000 0.14 0.14
+ATOM 2 X RES 1 0.777 0.875 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.053 -0.006 0.000 0.14 0.14
+ATOM 4 X RES 3 1.080 -0.264 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.276 1.115 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.755 -0.846 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.130 0.190 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0668 mds.2=0.0049
+ATOM 1 X RES 0 0.365 -1.083 0.000 0.14 0.14
+ATOM 2 X RES 1 0.796 0.906 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.054 -0.002 0.000 0.14 0.14
+ATOM 4 X RES 3 1.072 -0.255 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.298 1.121 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.767 -0.862 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.114 0.176 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0410 mds.2=0.0086
+ATOM 1 X RES 0 0.364 -1.107 0.000 0.14 0.14
+ATOM 2 X RES 1 0.813 0.930 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.042 0.003 0.000 0.14 0.14
+ATOM 4 X RES 3 1.059 -0.233 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.325 1.117 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.775 -0.883 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.094 0.172 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0264 mds.2=0.0110
+ATOM 1 X RES 0 0.349 -1.128 0.000 0.14 0.14
+ATOM 2 X RES 1 0.819 0.942 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.015 0.003 0.000 0.14 0.14
+ATOM 4 X RES 3 1.047 -0.201 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.347 1.111 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.775 -0.909 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.078 0.182 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0254 mds.2=0.0125
+ATOM 1 X RES 0 0.329 -1.141 0.000 0.14 0.14
+ATOM 2 X RES 1 0.815 0.935 0.000 0.14 0.14
+ATOM 3 X RES 2 0.019 0.004 0.000 0.14 0.14
+ATOM 4 X RES 3 1.043 -0.169 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.361 1.100 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.775 -0.923 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.070 0.193 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0503 mds.2=0.0085
+ATOM 1 X RES 0 0.302 -1.146 0.000 0.14 0.14
+ATOM 2 X RES 1 0.809 0.916 0.000 0.14 0.14
+ATOM 3 X RES 2 0.025 0.013 0.000 0.14 0.14
+ATOM 4 X RES 3 1.061 -0.149 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.367 1.087 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.763 -0.921 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.068 0.200 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0855 mds.2=0.0007
+ATOM 1 X RES 0 0.281 -1.138 0.000 0.14 0.14
+ATOM 2 X RES 1 0.789 0.899 0.000 0.14 0.14
+ATOM 3 X RES 2 0.013 0.023 0.000 0.14 0.14
+ATOM 4 X RES 3 1.095 -0.151 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.369 1.072 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.745 -0.909 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.063 0.205 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0975 mds.2=-0.0028
+ATOM 1 X RES 0 0.287 -1.119 0.000 0.14 0.14
+ATOM 2 X RES 1 0.767 0.882 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.006 0.027 0.000 0.14 0.14
+ATOM 4 X RES 3 1.125 -0.171 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.368 1.059 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.739 -0.892 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.066 0.214 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0983 mds.2=-0.0035
+ATOM 1 X RES 0 0.313 -1.090 0.000 0.14 0.14
+ATOM 2 X RES 1 0.738 0.869 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.011 0.018 0.000 0.14 0.14
+ATOM 4 X RES 3 1.148 -0.196 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.362 1.045 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.748 -0.863 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.078 0.217 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0997 mds.2=-0.0044
+ATOM 1 X RES 0 0.343 -1.052 0.000 0.14 0.14
+ATOM 2 X RES 1 0.705 0.860 0.000 0.14 0.14
+ATOM 3 X RES 2 0.001 -0.006 0.000 0.14 0.14
+ATOM 4 X RES 3 1.170 -0.224 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.356 1.037 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.763 -0.824 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.100 0.209 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0877 mds.2=-0.0021
+ATOM 1 X RES 0 0.383 -1.022 0.000 0.14 0.14
+ATOM 2 X RES 1 0.672 0.850 0.000 0.14 0.14
+ATOM 3 X RES 2 0.019 -0.028 0.000 0.14 0.14
+ATOM 4 X RES 3 1.187 -0.249 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.359 1.039 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.769 -0.790 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.132 0.199 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0501 mds.2=0.0053
+ATOM 1 X RES 0 0.418 -1.005 0.000 0.14 0.14
+ATOM 2 X RES 1 0.655 0.834 0.000 0.14 0.14
+ATOM 3 X RES 2 0.040 -0.032 0.000 0.14 0.14
+ATOM 4 X RES 3 1.208 -0.259 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.384 1.048 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.766 -0.777 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.172 0.191 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0104 mds.2=0.0140
+ATOM 1 X RES 0 0.453 -1.018 0.000 0.14 0.14
+ATOM 2 X RES 1 0.655 0.828 0.000 0.14 0.14
+ATOM 3 X RES 2 0.050 -0.020 0.000 0.14 0.14
+ATOM 4 X RES 3 1.228 -0.248 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.425 1.049 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.752 -0.784 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.208 0.194 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0199 mds.2=0.0221
+ATOM 1 X RES 0 0.482 -1.045 0.000 0.14 0.14
+ATOM 2 X RES 1 0.667 0.836 0.000 0.14 0.14
+ATOM 3 X RES 2 0.047 -0.010 0.000 0.14 0.14
+ATOM 4 X RES 3 1.238 -0.225 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.471 1.045 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.724 -0.808 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.238 0.207 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0416 mds.2=0.0277
+ATOM 1 X RES 0 0.504 -1.079 0.000 0.14 0.14
+ATOM 2 X RES 1 0.682 0.861 0.000 0.14 0.14
+ATOM 3 X RES 2 0.033 -0.018 0.000 0.14 0.14
+ATOM 4 X RES 3 1.247 -0.195 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.513 1.038 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.690 -0.830 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.263 0.222 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0688 mds.2=0.0338
+ATOM 1 X RES 0 0.523 -1.110 0.000 0.14 0.14
+ATOM 2 X RES 1 0.696 0.890 0.000 0.14 0.14
+ATOM 3 X RES 2 0.016 -0.029 0.000 0.14 0.14
+ATOM 4 X RES 3 1.260 -0.158 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.547 1.026 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.664 -0.850 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.284 0.232 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0858 mds.2=0.0354
+ATOM 1 X RES 0 0.529 -1.130 0.000 0.14 0.14
+ATOM 2 X RES 1 0.698 0.911 0.000 0.14 0.14
+ATOM 3 X RES 2 0.019 -0.034 0.000 0.14 0.14
+ATOM 4 X RES 3 1.265 -0.122 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.563 1.011 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.648 -0.868 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.299 0.232 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0897 mds.2=0.0313
+ATOM 1 X RES 0 0.528 -1.136 0.000 0.14 0.14
+ATOM 2 X RES 1 0.694 0.927 0.000 0.14 0.14
+ATOM 3 X RES 2 0.035 -0.023 0.000 0.14 0.14
+ATOM 4 X RES 3 1.262 -0.086 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.567 0.991 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.637 -0.889 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.315 0.216 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0920 mds.2=0.0254
+ATOM 1 X RES 0 0.528 -1.130 0.000 0.14 0.14
+ATOM 2 X RES 1 0.686 0.938 0.000 0.14 0.14
+ATOM 3 X RES 2 0.053 0.002 0.000 0.14 0.14
+ATOM 4 X RES 3 1.249 -0.048 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.561 0.967 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.631 -0.911 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.324 0.181 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.1168 mds.2=0.0227
+ATOM 1 X RES 0 0.534 -1.112 0.000 0.14 0.14
+ATOM 2 X RES 1 0.664 0.946 0.000 0.14 0.14
+ATOM 3 X RES 2 0.074 0.024 0.000 0.14 0.14
+ATOM 4 X RES 3 1.230 -0.012 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.550 0.943 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.623 -0.927 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.330 0.138 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.1447 mds.2=0.0227
+ATOM 1 X RES 0 0.543 -1.081 0.000 0.14 0.14
+ATOM 2 X RES 1 0.632 0.965 0.000 0.14 0.14
+ATOM 3 X RES 2 0.094 0.034 0.000 0.14 0.14
+ATOM 4 X RES 3 1.211 0.012 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.539 0.912 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.613 -0.935 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.329 0.093 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.1636 mds.2=0.0221
+ATOM 1 X RES 0 0.546 -1.042 0.000 0.14 0.14
+ATOM 2 X RES 1 0.597 0.993 0.000 0.14 0.14
+ATOM 3 X RES 2 0.116 0.021 0.000 0.14 0.14
+ATOM 4 X RES 3 1.190 0.022 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.530 0.875 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.599 -0.924 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.319 0.055 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.1461 mds.2=0.0182
+ATOM 1 X RES 0 0.547 -0.997 0.000 0.14 0.14
+ATOM 2 X RES 1 0.563 1.025 0.000 0.14 0.14
+ATOM 3 X RES 2 0.116 -0.009 0.000 0.14 0.14
+ATOM 4 X RES 3 1.175 0.027 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.526 0.852 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.576 -0.910 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.299 0.014 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.1212 mds.2=0.0139
+ATOM 1 X RES 0 0.560 -0.965 0.000 0.14 0.14
+ATOM 2 X RES 1 0.530 1.054 0.000 0.14 0.14
+ATOM 3 X RES 2 0.103 -0.036 0.000 0.14 0.14
+ATOM 4 X RES 3 1.171 0.030 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.534 0.833 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.554 -0.899 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.276 -0.018 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0775 mds.2=0.0056
+ATOM 1 X RES 0 0.585 -0.956 0.000 0.14 0.14
+ATOM 2 X RES 1 0.506 1.071 0.000 0.14 0.14
+ATOM 3 X RES 2 0.086 -0.031 0.000 0.14 0.14
+ATOM 4 X RES 3 1.164 0.040 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.555 0.812 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.542 -0.885 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.244 -0.051 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0008 mds.2=-0.0041
+ATOM 1 X RES 0 0.614 -0.960 0.000 0.14 0.14
+ATOM 2 X RES 1 0.479 1.070 0.000 0.14 0.14
+ATOM 3 X RES 2 0.067 0.000 0.000 0.14 0.14
+ATOM 4 X RES 3 1.155 0.052 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.586 0.807 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.534 -0.884 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.195 -0.085 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0469 mds.2=-0.0038
+ATOM 1 X RES 0 0.643 -0.966 0.000 0.14 0.14
+ATOM 2 X RES 1 0.445 1.058 0.000 0.14 0.14
+ATOM 3 X RES 2 0.061 0.027 0.000 0.14 0.14
+ATOM 4 X RES 3 1.143 0.061 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.630 0.824 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.510 -0.904 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.152 -0.100 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0771 mds.2=-0.0004
+ATOM 1 X RES 0 0.665 -0.965 0.000 0.14 0.14
+ATOM 2 X RES 1 0.419 1.048 0.000 0.14 0.14
+ATOM 3 X RES 2 0.053 0.037 0.000 0.14 0.14
+ATOM 4 X RES 3 1.135 0.063 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.675 0.857 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.476 -0.947 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.121 -0.094 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0917 mds.2=0.0005
+ATOM 1 X RES 0 0.668 -0.966 0.000 0.14 0.14
+ATOM 2 X RES 1 0.402 1.048 0.000 0.14 0.14
+ATOM 3 X RES 2 0.036 0.023 0.000 0.14 0.14
+ATOM 4 X RES 3 1.129 0.069 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.712 0.911 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.432 -0.995 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.091 -0.089 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0656 mds.2=0.0042
+ATOM 1 X RES 0 0.664 -0.969 0.000 0.14 0.14
+ATOM 2 X RES 1 0.386 1.048 0.000 0.14 0.14
+ATOM 3 X RES 2 0.021 -0.005 0.000 0.14 0.14
+ATOM 4 X RES 3 1.126 0.085 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.737 0.970 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.398 -1.040 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.063 -0.089 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0034 mds.2=0.0115
+ATOM 1 X RES 0 0.674 -0.967 0.000 0.14 0.14
+ATOM 2 X RES 1 0.367 1.050 0.000 0.14 0.14
+ATOM 3 X RES 2 0.010 -0.036 0.000 0.14 0.14
+ATOM 4 X RES 3 1.124 0.103 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.754 1.025 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.382 -1.074 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.037 -0.102 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0901 mds.2=0.0141
+ATOM 1 X RES 0 0.680 -0.954 0.000 0.14 0.14
+ATOM 2 X RES 1 0.358 1.047 0.000 0.14 0.14
+ATOM 3 X RES 2 0.021 -0.063 0.000 0.14 0.14
+ATOM 4 X RES 3 1.119 0.116 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.765 1.076 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.385 -1.095 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.028 -0.128 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.1784 mds.2=0.0069
+ATOM 1 X RES 0 0.690 -0.938 0.000 0.14 0.14
+ATOM 2 X RES 1 0.347 1.029 0.000 0.14 0.14
+ATOM 3 X RES 2 0.051 -0.078 0.000 0.14 0.14
+ATOM 4 X RES 3 1.116 0.135 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.772 1.116 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.402 -1.110 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.030 -0.154 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.2253 mds.2=-0.0077
+ATOM 1 X RES 0 0.706 -0.946 0.000 0.14 0.14
+ATOM 2 X RES 1 0.343 1.008 0.000 0.14 0.14
+ATOM 3 X RES 2 0.072 -0.077 0.000 0.14 0.14
+ATOM 4 X RES 3 1.117 0.160 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.778 1.146 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.421 -1.111 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.039 -0.181 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.2372 mds.2=-0.0248
+ATOM 1 X RES 0 0.720 -0.971 0.000 0.14 0.14
+ATOM 2 X RES 1 0.341 0.990 0.000 0.14 0.14
+ATOM 3 X RES 2 0.079 -0.070 0.000 0.14 0.14
+ATOM 4 X RES 3 1.120 0.191 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.780 1.169 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.430 -1.103 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.051 -0.207 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.2415 mds.2=-0.0448
+ATOM 1 X RES 0 0.727 -0.998 0.000 0.14 0.14
+ATOM 2 X RES 1 0.345 0.974 0.000 0.14 0.14
+ATOM 3 X RES 2 0.069 -0.070 0.000 0.14 0.14
+ATOM 4 X RES 3 1.138 0.217 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.790 1.191 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.430 -1.088 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.058 -0.226 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.2562 mds.2=-0.0539
+ATOM 1 X RES 0 0.735 -1.020 0.000 0.14 0.14
+ATOM 2 X RES 1 0.350 0.977 0.000 0.14 0.14
+ATOM 3 X RES 2 0.050 -0.082 0.000 0.14 0.14
+ATOM 4 X RES 3 1.152 0.229 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.804 1.204 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.422 -1.076 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.060 -0.232 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.2901 mds.2=-0.0433
+ATOM 1 X RES 0 0.740 -1.029 0.000 0.14 0.14
+ATOM 2 X RES 1 0.352 0.986 0.000 0.14 0.14
+ATOM 3 X RES 2 0.031 -0.099 0.000 0.14 0.14
+ATOM 4 X RES 3 1.165 0.226 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.816 1.210 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.407 -1.081 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.065 -0.213 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.3173 mds.2=-0.0215
+ATOM 1 X RES 0 0.744 -1.029 0.000 0.14 0.14
+ATOM 2 X RES 1 0.344 0.999 0.000 0.14 0.14
+ATOM 3 X RES 2 0.030 -0.112 0.000 0.14 0.14
+ATOM 4 X RES 3 1.168 0.219 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.825 1.209 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.388 -1.105 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.074 -0.181 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.3117 mds.2=0.0096
+ATOM 1 X RES 0 0.751 -1.025 0.000 0.14 0.14
+ATOM 2 X RES 1 0.330 1.013 0.000 0.14 0.14
+ATOM 3 X RES 2 0.031 -0.118 0.000 0.14 0.14
+ATOM 4 X RES 3 1.170 0.205 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.818 1.200 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.371 -1.138 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.092 -0.139 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.2787 mds.2=0.0317
+ATOM 1 X RES 0 0.756 -1.011 0.000 0.14 0.14
+ATOM 2 X RES 1 0.311 1.017 0.000 0.14 0.14
+ATOM 3 X RES 2 0.028 -0.123 0.000 0.14 0.14
+ATOM 4 X RES 3 1.165 0.185 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.794 1.183 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.355 -1.159 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.111 -0.092 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.2319 mds.2=0.0372
+ATOM 1 X RES 0 0.755 -0.994 0.000 0.14 0.14
+ATOM 2 X RES 1 0.293 1.014 0.000 0.14 0.14
+ATOM 3 X RES 2 0.029 -0.123 0.000 0.14 0.14
+ATOM 4 X RES 3 1.157 0.163 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.766 1.163 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.344 -1.176 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.125 -0.047 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.1897 mds.2=0.0305
+ATOM 1 X RES 0 0.749 -0.971 0.000 0.14 0.14
+ATOM 2 X RES 1 0.285 1.005 0.000 0.14 0.14
+ATOM 3 X RES 2 0.029 -0.124 0.000 0.14 0.14
+ATOM 4 X RES 3 1.146 0.138 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.747 1.135 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.331 -1.192 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.131 0.010 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.1592 mds.2=0.0142
+ATOM 1 X RES 0 0.751 -0.939 0.000 0.14 0.14
+ATOM 2 X RES 1 0.299 0.985 0.000 0.14 0.14
+ATOM 3 X RES 2 0.027 -0.125 0.000 0.14 0.14
+ATOM 4 X RES 3 1.133 0.113 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.756 1.096 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.324 -1.196 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.129 0.066 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.1212 mds.2=-0.0049
+ATOM 1 X RES 0 0.757 -0.914 0.000 0.14 0.14
+ATOM 2 X RES 1 0.331 0.973 0.000 0.14 0.14
+ATOM 3 X RES 2 0.019 -0.122 0.000 0.14 0.14
+ATOM 4 X RES 3 1.116 0.092 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.774 1.059 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.321 -1.195 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.128 0.107 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0960 mds.2=-0.0150
+ATOM 1 X RES 0 0.766 -0.904 0.000 0.14 0.14
+ATOM 2 X RES 1 0.356 0.964 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.002 -0.114 0.000 0.14 0.14
+ATOM 4 X RES 3 1.107 0.082 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.776 1.061 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.313 -1.196 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.139 0.106 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0842 mds.2=-0.0162
+ATOM 1 X RES 0 0.773 -0.914 0.000 0.14 0.14
+ATOM 2 X RES 1 0.384 0.954 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.033 -0.101 0.000 0.14 0.14
+ATOM 4 X RES 3 1.098 0.089 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.762 1.089 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.296 -1.191 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.164 0.074 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0813 mds.2=-0.0187
+ATOM 1 X RES 0 0.773 -0.937 0.000 0.14 0.14
+ATOM 2 X RES 1 0.416 0.945 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.064 -0.080 0.000 0.14 0.14
+ATOM 4 X RES 3 1.093 0.104 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.746 1.119 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.278 -1.187 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.195 0.036 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0823 mds.2=-0.0193
+ATOM 1 X RES 0 0.771 -0.955 0.000 0.14 0.14
+ATOM 2 X RES 1 0.444 0.951 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.089 -0.068 0.000 0.14 0.14
+ATOM 4 X RES 3 1.085 0.120 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.726 1.137 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.268 -1.189 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.217 0.004 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0773 mds.2=-0.0179
+ATOM 1 X RES 0 0.771 -0.964 0.000 0.14 0.14
+ATOM 2 X RES 1 0.456 0.969 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.102 -0.051 0.000 0.14 0.14
+ATOM 4 X RES 3 1.085 0.115 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.695 1.144 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.283 -1.189 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.231 -0.025 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0621 mds.2=-0.0202
+ATOM 1 X RES 0 0.776 -0.960 0.000 0.14 0.14
+ATOM 2 X RES 1 0.451 0.999 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.102 -0.025 0.000 0.14 0.14
+ATOM 4 X RES 3 1.090 0.096 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.663 1.134 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.309 -1.199 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.244 -0.046 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0449 mds.2=-0.0215
+ATOM 1 X RES 0 0.776 -0.948 0.000 0.14 0.14
+ATOM 2 X RES 1 0.443 1.030 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.097 0.001 0.000 0.14 0.14
+ATOM 4 X RES 3 1.097 0.071 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.639 1.115 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.329 -1.206 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.252 -0.063 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0269 mds.2=-0.0307
+ATOM 1 X RES 0 0.763 -0.931 0.000 0.14 0.14
+ATOM 2 X RES 1 0.444 1.047 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.073 0.025 0.000 0.14 0.14
+ATOM 4 X RES 3 1.099 0.057 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.631 1.091 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.348 -1.217 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.253 -0.072 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=-0.0075 mds.2=-0.0368
+ATOM 1 X RES 0 0.728 -0.927 0.000 0.14 0.14
+ATOM 2 X RES 1 0.459 1.047 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.043 0.037 0.000 0.14 0.14
+ATOM 4 X RES 3 1.083 0.065 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.626 1.066 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.362 -1.214 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.238 -0.074 0.000 0.14 0.14
+END
+DESCRIPTION: analysis data from calculation done at time 10.000000
+REMARK WEIGHT=1.0000 TYPE=EUCLIDEAN
+REMARK PROPERTIES=mds.1,mds.2
+REMARK mds.1=0.0266 mds.2=-0.0342
+ATOM 1 X RES 0 0.677 -0.922 0.000 0.14 0.14
+ATOM 2 X RES 1 0.475 1.034 0.000 0.14 0.14
+ATOM 3 X RES 2 -0.022 0.038 0.000 0.14 0.14
+ATOM 4 X RES 3 1.067 0.089 0.000 0.14 0.14
+ATOM 5 X RES 4 -0.617 1.031 0.000 0.14 0.14
+ATOM 6 X RES 5 -0.375 -1.199 0.000 0.14 0.14
+ATOM 7 X RES 6 -1.204 -0.071 0.000 0.14 0.14
+END
diff --git a/regtest/dimred/rt-mds2/in b/regtest/dimred/rt-mds2/in
new file mode 100644
index 000000000..030417936
--- /dev/null
+++ b/regtest/dimred/rt-mds2/in
@@ -0,0 +1,11 @@
+inputfile input.xyz
+outputfile output.xyz
+temperature 0.2
+tstep 0.005
+friction 1
+forcecutoff 2.5
+listcutoff 3.0
+ndim 2
+nstep 2000
+nconfig 1000 trajectory.xyz
+nstat 1000 energies.dat
diff --git a/regtest/dimred/rt-mds2/input.xyz b/regtest/dimred/rt-mds2/input.xyz
new file mode 100644
index 000000000..9e1e59174
--- /dev/null
+++ b/regtest/dimred/rt-mds2/input.xyz
@@ -0,0 +1,9 @@
+7
+100. 100. 100.
+Ar 7.3933470660 -2.6986483924 0.0000000000
+Ar 7.8226765198 -0.7390907295 0.0000000000
+Ar 7.1014969839 -1.6164766614 0.0000000000
+Ar 8.2357184242 -1.7097824975 0.0000000000
+Ar 6.7372520842 -0.5111536183 0.0000000000
+Ar 6.3777119489 -2.4640437401 0.0000000000
+Ar 5.9900631495 -1.3385375043 0.0000000000
diff --git a/regtest/dimred/rt-mds2/list_embed.reference b/regtest/dimred/rt-mds2/list_embed.reference
new file mode 100644
index 000000000..b24c465df
--- /dev/null
+++ b/regtest/dimred/rt-mds2/list_embed.reference
@@ -0,0 +1,101 @@
+#! FIELDS mds.1 mds.2
+ 0.0594 0.0053
+ 0.0683 0.0034
+ 0.0705 0.0006
+ 0.0729 -0.0019
+ 0.0874 -0.0069
+ 0.0961 -0.0095
+ 0.0867 -0.0062
+ 0.0719 -0.0008
+ 0.0575 0.0031
+ 0.0552 0.0034
+ 0.0682 -0.0002
+ 0.0781 -0.0024
+ 0.0785 -0.0025
+ 0.0763 -0.0027
+ 0.0755 -0.0041
+ 0.0792 -0.0069
+ 0.0778 -0.0062
+ 0.0727 -0.0025
+ 0.0726 0.0014
+ 0.0756 0.0030
+ 0.0821 0.0017
+ 0.0816 0.0001
+ 0.0774 0.0008
+ 0.0766 0.0008
+ 0.0838 -0.0005
+ 0.0931 -0.0016
+ 0.0936 -0.0010
+ 0.0923 -0.0009
+ 0.0906 -0.0008
+ 0.0706 0.0025
+ 0.0664 0.0050
+ 0.0901 0.0019
+ 0.1059 -0.0015
+ 0.0917 0.0006
+ 0.0876 0.0021
+ 0.1008 -0.0001
+ 0.0955 -0.0014
+ 0.0858 -0.0018
+ 0.0894 -0.0005
+ 0.0922 0.0014
+ 0.0917 0.0010
+ 0.0925 -0.0043
+ 0.0967 -0.0102
+ 0.1073 -0.0096
+ 0.1065 -0.0047
+ 0.0935 -0.0003
+ 0.0668 0.0049
+ 0.0410 0.0086
+ 0.0264 0.0110
+ 0.0254 0.0125
+ 0.0503 0.0085
+ 0.0855 0.0007
+ 0.0975 -0.0028
+ 0.0983 -0.0035
+ 0.0997 -0.0044
+ 0.0877 -0.0021
+ 0.0501 0.0053
+ 0.0104 0.0140
+ -0.0199 0.0221
+ -0.0416 0.0277
+ -0.0688 0.0338
+ -0.0858 0.0354
+ -0.0897 0.0313
+ -0.0920 0.0254
+ -0.1168 0.0227
+ -0.1447 0.0227
+ -0.1636 0.0221
+ -0.1461 0.0182
+ -0.1212 0.0139
+ -0.0775 0.0056
+ -0.0008 -0.0041
+ 0.0469 -0.0038
+ 0.0771 -0.0004
+ 0.0917 0.0005
+ 0.0656 0.0042
+ -0.0034 0.0115
+ -0.0901 0.0141
+ -0.1784 0.0069
+ -0.2253 -0.0077
+ -0.2372 -0.0248
+ -0.2415 -0.0448
+ -0.2562 -0.0539
+ -0.2901 -0.0433
+ -0.3173 -0.0215
+ -0.3117 0.0096
+ -0.2787 0.0317
+ -0.2319 0.0372
+ -0.1897 0.0305
+ -0.1592 0.0142
+ -0.1212 -0.0049
+ -0.0960 -0.0150
+ -0.0842 -0.0162
+ -0.0813 -0.0187
+ -0.0823 -0.0193
+ -0.0773 -0.0179
+ -0.0621 -0.0202
+ -0.0449 -0.0215
+ -0.0269 -0.0307
+ -0.0075 -0.0368
+ 0.0266 -0.0342
diff --git a/regtest/dimred/rt-mds2/plumed.dat b/regtest/dimred/rt-mds2/plumed.dat
new file mode 100755
index 000000000..50b1e03fb
--- /dev/null
+++ b/regtest/dimred/rt-mds2/plumed.dat
@@ -0,0 +1,30 @@
+UNITS NATURAL
+COM ATOMS=1-7 LABEL=com
+DISTANCE ATOMS=1,com LABEL=d1
+UPPER_WALLS ARG=d1 AT=2.0 KAPPA=100.
+DISTANCE ATOMS=2,com LABEL=d2
+UPPER_WALLS ARG=d2 AT=2.0 KAPPA=100.
+DISTANCE ATOMS=3,com LABEL=d3
+UPPER_WALLS ARG=d3 AT=2.0 KAPPA=100.
+DISTANCE ATOMS=4,com LABEL=d4
+UPPER_WALLS ARG=d4 AT=2.0 KAPPA=100.
+DISTANCE ATOMS=5,com LABEL=d5
+UPPER_WALLS ARG=d5 AT=2.0 KAPPA=100.
+DISTANCE ATOMS=6,com LABEL=d6
+UPPER_WALLS ARG=d6 AT=2.0 KAPPA=100.
+DISTANCE ATOMS=7,com LABEL=d7
+UPPER_WALLS ARG=d7 AT=2.0 KAPPA=100.
+
+COORDINATIONNUMBER SPECIES=1-7 MOMENTS=2-3 SWITCH={RATIONAL R_0=1.5 NN=8 MM=16} LABEL=c1
+
+ff: COLLECT_FRAMES ATOMS=1-7 STRIDE=10 RUN=1000
+oo: EUCLIDEAN_DISSIMILARITIES ARG=c1.moment-2,c1.moment-3 FRAMES=ff
+
+CLASSICAL_MDS ...
+ USE_OUTPUT_DATA_FROM=oo
+ NLOW_DIM=2
+ LABEL=mds
+... CLASSICAL_MDS
+
+OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=mds FILE=list_embed FMT=%8.4f
+OUTPUT_ANALYSIS_DATA_TO_PDB USE_OUTPUT_DATA_FROM=mds FILE=embed FMT=%8.4f
diff --git a/src/analysis/AnalysisBase.cpp b/src/analysis/AnalysisBase.cpp
index deda1e0ca..c2e1186f5 100644
--- a/src/analysis/AnalysisBase.cpp
+++ b/src/analysis/AnalysisBase.cpp
@@ -52,7 +52,7 @@ mydata(NULL)
if( datastr.length()>0 ){
mydata=plumed.getActionSet().selectWithLabel<AnalysisBase*>( datastr );
ReadAnalysisFrames* checkt = dynamic_cast<ReadAnalysisFrames*>( mydata );
- if( checkt ) error("READ_ANALYSIS_FRAMES should only be used in association with READ_DISSSIMILARITY_MATRIX");
+ if( checkt ) error("READ_ANALYSIS_FRAMES should only be used in input to the FRAMES keyword");
log.printf(" performing analysis on output from %s \n",datastr.c_str() );
if( !mydata ) error("could not find analysis action named " + datastr );
freq=mydata->freq; use_all_data=mydata->use_all_data;
diff --git a/src/analysis/AnalysisBase.h b/src/analysis/AnalysisBase.h
index 0708954e3..9208463ae 100644
--- a/src/analysis/AnalysisBase.h
+++ b/src/analysis/AnalysisBase.h
@@ -85,8 +85,6 @@ public:
virtual void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Get a reference configuration (in dimensionality reduction this returns the projection)
virtual ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata );
-/// Get the input configuration (in dimensionality reduction this returns the high dimensional configuration)
- virtual ReferenceConfiguration* getInputReferenceConfiguration( const unsigned& idata );
/// This actually performs the analysis
virtual void performAnalysis()=0;
/// These overwrite things from inherited classes (this is a bit of a fudge)
@@ -170,11 +168,6 @@ ReferenceConfiguration* AnalysisBase::getReferenceConfiguration( const unsigned&
return mydata->getReferenceConfiguration( idata );
}
-inline
-ReferenceConfiguration* AnalysisBase::getInputReferenceConfiguration( const unsigned& idata ){
- return mydata->getInputReferenceConfiguration( idata );
-}
-
}
}
diff --git a/src/analysis/AnalysisWithDataCollection.cpp b/src/analysis/AnalysisWithDataCollection.cpp
index 71afb441d..361f88ccf 100644
--- a/src/analysis/AnalysisWithDataCollection.cpp
+++ b/src/analysis/AnalysisWithDataCollection.cpp
@@ -46,6 +46,9 @@ void AnalysisWithDataCollection::registerKeywords( Keywords& keys ){
keys.addFlag("USE_ALL_DATA",false,"just analyse all the data in the trajectory. This option should be used in tandem with ATOMS/ARG + STRIDE");
keys.addFlag("REWEIGHT_BIAS",false,"reweight the data using all the biases acting on the dynamics. This option must be used in tandem with ATOMS/ARG + STRIDE + RUN/USE_ALL_DATA. "
"For more information see \\ref analysisbas");
+ keys.reserve("optional","FRAMES","with this keyword you can specify the atomic configurations that you would like to store using "
+ "an COLLECT_FRAMES action. When the projection is output in dimensionality reduction you will then "
+ "print the underlying atoms and their projection");
keys.add("optional","REWEIGHT_TEMP","reweight data from a trajectory at one temperature and output the probability distribution at a second temperature. This option must be used in tandem with ATOMS/ARG + STRIDE + RUN/USE_ALL_DATA. "
"For more information see \\ref analysisbas");
keys.add("optional","TEMP","the system temperature. This is required if you are reweighting (REWEIGHT_BIAS/REWEIGHT_TEMP) or if you are calculating free energies. You are not required to specify the temperature if this is passed by the underlying MD code.");
@@ -63,13 +66,25 @@ write_chq(false),
rtemp(0),
idata(0),
firstAnalysisDone(false),
-old_norm(0.0)
+old_norm(0.0),
+myframes(NULL)
{
if( !mydata ){
+ // Check for FRAMES keyword that allows us to read reference configurations from elsewhere
+ std::string instring; if( keywords.exists("FRAMES") ) parse("FRAMES",instring);
+ if( instring.length()>0 ){
+ if( mydata ) error("frames keyword is not compatible with USE_OUTPUT_DATA_FROM");
+ myframes=plumed.getActionSet().selectWithLabel<ReadAnalysisFrames*>( instring );
+ if( !myframes ) error( instring + " is not the name of an object that collects trajectory data");
+ log.printf(" frames are stored by object with label %s \n",instring.c_str() );
+ freq=myframes->freq; use_all_data=myframes->use_all_data; setStride( myframes->getStride() );
+ }
+
// Check if we are using the input data from another action
std::string datastr;
if( keywords.exists("REUSE_INPUT_DATA_FROM") ) parse("REUSE_INPUT_DATA_FROM",datastr);
if( datastr.length()>0 ) {
+ if( myframes ) error("FRAMES command is incompatible with REUSE_INPUT_DATA_FROM");
AnalysisWithDataCollection* checkd = plumed.getActionSet().selectWithLabel<AnalysisWithDataCollection*>( datastr );
if( !checkd) error("cannot reuse input data from action with label " + datastr + " as this does not store data");
ReadAnalysisFrames* checkt = dynamic_cast<ReadAnalysisFrames*>( checkd );
@@ -129,31 +144,49 @@ old_norm(0.0)
metricname="";
}
- // Read in the information about how often to run the analysis (storage is read in in ActionPilot.cpp)
- if( keywords.exists("USE_ALL_DATA") ){
- if( !keywords.exists("RUN") ) use_all_data=true;
- else parseFlag("USE_ALL_DATA",use_all_data);
- }
- if(!use_all_data){
- if( keywords.exists("RUN") ) parse("RUN",freq);
- // Setup everything given the ammount of data that we will have in each analysis
- if( freq%getStride()!= 0 ) error("Frequncy of running is not a multiple of the stride");
- unsigned ndata=freq/getStride(); data.resize(ndata); logweights.resize( ndata );
- for(unsigned i=0;i<ndata;++i) data[i]=metricRegister().create<ReferenceConfiguration>( metricname );
- log.printf(" running analysis every %u steps\n",freq);
- // Check if we are doing block averaging
- nomemory=false;
- if( keywords.exists("NOMEMORY") ) parseFlag("NOMEMORY",nomemory);
- if(nomemory) log.printf(" doing block averaging and analysing each portion of trajectory separately\n");
+ bool dobias;
+ if( !myframes ){
+ // Read in the information about how often to run the analysis (storage is read in in ActionPilot.cpp)
+ if( keywords.exists("USE_ALL_DATA") ){
+ if( !keywords.exists("RUN") ) use_all_data=true;
+ else parseFlag("USE_ALL_DATA",use_all_data);
+ }
+ if(!use_all_data){
+ if( keywords.exists("RUN") ) parse("RUN",freq);
+ // Setup everything given the ammount of data that we will have in each analysis
+ if( freq%getStride()!= 0 ) error("Frequncy of running is not a multiple of the stride");
+ // Check if we are doing block averaging
+ nomemory=false;
+ if( keywords.exists("NOMEMORY") ) parseFlag("NOMEMORY",nomemory);
+ if(nomemory) log.printf(" doing block averaging and analysing each portion of trajectory separately\n");
+ } else {
+ log.printf(" analysing all data in trajectory\n");
+ }
+
+ // Read in stuff for reweighting of trajectories
+
+ // Reweighting for biases
+ if( keywords.exists("REWEIGHT_BIAS") ) parseFlag("REWEIGHT_BIAS",dobias);
+
+ // Reweighting for temperatures
+ rtemp=0;
+ if( keywords.exists("REWEIGHT_TEMP") ) parse("REWEIGHT_TEMP",rtemp);
+ if( rtemp!=0 ){
+ rtemp*=plumed.getAtoms().getKBoltzmann();
+ log.printf(" reweighting simulation to probabilities at temperature %f\n",rtemp);
+ }
+ // Now retrieve the temperature in the simulation
+ simtemp=0;
+ if( keywords.exists("TEMP") ) parse("TEMP",simtemp);
+ if(simtemp>0) simtemp*=plumed.getAtoms().getKBoltzmann();
+ else simtemp=plumed.getAtoms().getKbT();
+ if(simtemp==0 && (rtemp!=0 || !biases.empty()) ) error("The MD engine does not pass the temperature to plumed so you have to specify it using TEMP");
} else {
- log.printf(" analysing all data in trajectory\n");
+ nomemory = myframes->nomemory; dobias = (myframes->biases.size()>0);
+ rtemp = myframes->rtemp; simtemp = myframes->simtemp;
}
- // Read in stuff for reweighting of trajectories
-
- // Reweighting for biases
- bool dobias;
- if( keywords.exists("REWEIGHT_BIAS") ) parseFlag("REWEIGHT_BIAS",dobias);
+ // Setup bias reweighting
if( dobias ){
std::vector<ActionWithValue*> all=plumed.getActionSet().select<ActionWithValue*>();
if( all.empty() ) error("your input file is not telling plumed to calculate anything");
@@ -171,20 +204,13 @@ old_norm(0.0)
if( biases.empty() ) error("you are asking to reweight bias but there does not appear to be a bias acting on your system");
requestArguments( arg );
}
-
- // Reweighting for temperatures
- rtemp=0;
- if( keywords.exists("REWEIGHT_TEMP") ) parse("REWEIGHT_TEMP",rtemp);
- if( rtemp!=0 ){
- rtemp*=plumed.getAtoms().getKBoltzmann();
- log.printf(" reweighting simulation to probabilities at temperature %f\n",rtemp);
+ // Setup reference configuration objects to store data
+ if( !use_all_data ){
+ plumed_assert( !mydata );
+ log.printf(" running analysis every %u steps\n",freq);
+ unsigned ndata=freq/getStride(); data.resize(ndata); logweights.resize( ndata );
+ for(unsigned i=0;i<ndata;++i) data[i]=metricRegister().create<ReferenceConfiguration>( metricname );
}
- // Now retrieve the temperature in the simulation
- simtemp=0;
- if( keywords.exists("TEMP") ) parse("TEMP",simtemp);
- if(simtemp>0) simtemp*=plumed.getAtoms().getKBoltzmann();
- else simtemp=plumed.getAtoms().getKbT();
- if(simtemp==0 && (rtemp!=0 || !biases.empty()) ) error("The MD engine does not pass the temperature to plumed so you have to specify it using TEMP");
// Check if a check point is required (this should be got rid of at some point when we have proper checkpointing) GAT
if( keywords.exists("WRITE_CHECKPOINT") ) parseFlag("WRITE_CHECKPOINT",write_chq);
@@ -207,8 +233,8 @@ old_norm(0.0)
for(unsigned i=0;i<getNumberOfArguments();++i) rfile.setupPrintValue( getPntrToArgument(i) );
}
// This is the end of the stuff for the checkpoint file - hopefully get rid of all this in not too distant future GAT
- }
- }
+ }
+ }
}
AnalysisWithDataCollection::~AnalysisWithDataCollection(){
@@ -264,15 +290,14 @@ void AnalysisWithDataCollection::getDataPoint( const unsigned& idat, std::vector
}
ReferenceConfiguration* AnalysisWithDataCollection::getReferenceConfiguration( const unsigned& idat ){
- if( !mydata ){ plumed_dbg_assert( idat<data.size() ); return data[idat]; }
+ if( !mydata ){
+ plumed_dbg_assert( idat<data.size() );
+ if( myframes ) return myframes->getReferenceConfiguration( idat );
+ return data[idat];
+ }
return AnalysisBase::getReferenceConfiguration( idat );
}
-ReferenceConfiguration* AnalysisWithDataCollection::getInputReferenceConfiguration( const unsigned& idat ){
- if( !mydata ){ plumed_dbg_assert( idat<data.size() ); return data[idat]; }
- return AnalysisBase::getInputReferenceConfiguration( idat );
-}
-
void AnalysisWithDataCollection::update(){
if( mydata ){ AnalysisBase::update(); return; }
// Ignore first bit of data if we are not using all data - this is a weird choice - I am not sure I understand GAT (perhaps this should be changed)?
diff --git a/src/analysis/AnalysisWithDataCollection.h b/src/analysis/AnalysisWithDataCollection.h
index 97e2ae74c..8697ea147 100644
--- a/src/analysis/AnalysisWithDataCollection.h
+++ b/src/analysis/AnalysisWithDataCollection.h
@@ -31,7 +31,11 @@ class ReferenceConfiguration;
namespace analysis {
+class ReadAnalysisFrames;
+
class AnalysisWithDataCollection : public AnalysisBase {
+friend class EuclideanDissimilarityMatrix;
+friend class ReadDissimilarityMatrix;
private:
/// Are we treating each block of data separately
bool nomemory;
@@ -53,6 +57,9 @@ private:
bool firstAnalysisDone;
/// The value of the old normalization constant
double norm, old_norm;
+/// This allows you to output trajectory data with the projections
+/// in EUCLIDEAN_DISSIMLAIRITIES and READ_DISSIMILARITY_MATRIX
+ ReadAnalysisFrames* myframes;
/// Data is collected from the trajectory by passing it to this pdb. These pdb
/// files are then read by the ReferenceConfigurations in data
PDB mypdb;
@@ -93,8 +100,6 @@ public:
virtual void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Get a reference configuration (in dimensionality reduction this returns the projection)
virtual ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat );
-/// Get the underlying reference configuration (in dimensionality reduction this return the high dimensional point)
- ReferenceConfiguration* getInputReferenceConfiguration( const unsigned& idat );
/// This ensures that the energy is stored if we are reweighting
void prepare();
/// This stores the data and calls the analysis to be performed
diff --git a/src/analysis/EuclideanDissimilarityMatrix.cpp b/src/analysis/EuclideanDissimilarityMatrix.cpp
index d8d8ac568..5594bb347 100644
--- a/src/analysis/EuclideanDissimilarityMatrix.cpp
+++ b/src/analysis/EuclideanDissimilarityMatrix.cpp
@@ -55,7 +55,7 @@ PLUMED_REGISTER_ACTION(EuclideanDissimilarityMatrix,"EUCLIDEAN_DISSIMILARITIES")
void EuclideanDissimilarityMatrix::registerKeywords( Keywords& keys ){
AnalysisWithDataCollection::registerKeywords( keys );
- keys.reset_style("METRIC","atoms-1");
+ keys.reset_style("METRIC","atoms-1"); keys.use("FRAMES");
}
EuclideanDissimilarityMatrix::EuclideanDissimilarityMatrix( const ActionOptions& ao ):
@@ -72,8 +72,15 @@ void EuclideanDissimilarityMatrix::performAnalysis(){
double EuclideanDissimilarityMatrix::getDissimilarity( const unsigned& iframe, const unsigned& jframe ){
plumed_dbg_assert( iframe<dissimilarities.nrows() && jframe<dissimilarities.ncols() );
if( dissimilarities(iframe,jframe)>0. ){ return dissimilarities(iframe,jframe); }
- if( iframe!=jframe ){
- dissimilarities(iframe,jframe) = dissimilarities(jframe,iframe) = distance( getPbc(), getArguments(), getReferenceConfiguration(iframe), getReferenceConfiguration(jframe), true );
+ if( iframe!=jframe ){
+ ReferenceConfiguration* myref1; ReferenceConfiguration* myref2;
+ if( mydata ){ myref1=AnalysisBase::getReferenceConfiguration(iframe); myref2=AnalysisBase::getReferenceConfiguration(jframe); }
+ else { myref1 = data[iframe]; myref2 = data[jframe]; }
+ if( myref1->getNumberOfProperties()>0 ){
+ dissimilarities(iframe,jframe) = dissimilarities(jframe,iframe) = property_distance( myref1, myref2, true );
+ } else {
+ dissimilarities(iframe,jframe) = dissimilarities(jframe,iframe) = distance( getPbc(), getArguments(), myref1, myref2, true );
+ }
return dissimilarities(iframe,jframe);
}
return 0.0;
diff --git a/src/analysis/ReadAnalysisFrames.cpp b/src/analysis/ReadAnalysisFrames.cpp
index e6afb86f0..ea9c5c4ec 100644
--- a/src/analysis/ReadAnalysisFrames.cpp
+++ b/src/analysis/ReadAnalysisFrames.cpp
@@ -24,7 +24,7 @@
#include "core/ActionSet.h"
#include "core/ActionRegister.h"
-//+PLUMEDOC ANALYSIS READ_ANALYSIS_FRAMES
+//+PLUMEDOC ANALYSIS COLLECT_FRAMES
/*
This allows you to convert a trajectory and a dissimilarity matrix into a dissimilarity object
@@ -36,21 +36,17 @@ This allows you to convert a trajectory and a dissimilarity matrix into a dissim
namespace PLMD {
namespace analysis {
-PLUMED_REGISTER_ACTION(ReadAnalysisFrames,"READ_ANALYSIS_FRAMES")
+PLUMED_REGISTER_ACTION(ReadAnalysisFrames,"COLLECT_FRAMES")
void ReadAnalysisFrames::registerKeywords( Keywords& keys ){
AnalysisWithDataCollection::registerKeywords( keys );
- keys.reset_style("USE_ALL_DATA","hidden"); keys.remove("RUN"); keys.remove("REWEIGHT_BIAS"); keys.remove("REWEIGHT_TEMP");
- keys.remove("TEMP"); keys.remove("WRITE_CHECKPOINT"); keys.remove("NOMEMORY"); keys.remove("RESTART");
- keys.remove("UPDATE_FROM"); keys.remove("UPDATE_UNTIL"); keys.remove("USE_OUTPUT_DATA_FROM");
- keys.remove("ARG"); keys.remove("SERIAL"); keys.remove("REUSE_INPUT_DATA_FROM");
+ keys.remove("ARG"); keys.remove("SERIAL"); keys.remove("USE_OUTPUT_DATA_FROM");
}
ReadAnalysisFrames::ReadAnalysisFrames( const ActionOptions& ao ):
Action(ao),
AnalysisWithDataCollection(ao)
{
- if( plumed.getActionSet().size()!=0 ) error("read analysis frames command must be at top of input file");
}
}
diff --git a/src/analysis/ReadDissimilarityMatrix.cpp b/src/analysis/ReadDissimilarityMatrix.cpp
index 41905756f..b590488ed 100644
--- a/src/analysis/ReadDissimilarityMatrix.cpp
+++ b/src/analysis/ReadDissimilarityMatrix.cpp
@@ -50,7 +50,6 @@ public:
unsigned getNumberOfDataPoints() const ;
/// This gives an error as if we read in the matrix we dont have the coordinates
ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata );
- ReferenceConfiguration* getInputReferenceConfiguration( const unsigned& idata );
/// This gives an error as if we read in the matrix we dont have the coordinates
void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Tell everyone we have dissimilarities
@@ -72,7 +71,9 @@ PLUMED_REGISTER_ACTION(ReadDissimilarityMatrix,"READ_DISSIMILARITY_MATRIX")
void ReadDissimilarityMatrix::registerKeywords( Keywords& keys ){
AnalysisBase::registerKeywords( keys ); keys.remove("USE_OUTPUT_DATA_FROM");
keys.add("compulsory","FILE","an input file containing the matrix of dissimilarities");
- keys.add("optional","TRAJ","the label for a READ_ANALYSIS_FRAMES action that stores the trajectory");
+ keys.add("optional","FRAMES","with this keyword you can specify the atomic configurations that you would like to store using "
+ "an COLLECT_FRAMES action. When the projection is output in dimensionality reduction you will then "
+ "print the underlying atoms and their projection");
keys.add("optional","WFILE","input file containing weights of points");
}
@@ -81,11 +82,11 @@ Action(ao),
AnalysisBase(ao),
nnodes(1)
{
- std::string mytraj; parse("TRAJ",mytraj);
+ std::string mytraj; parse("FRAMES",mytraj);
if( mytraj.length()>0 ){
ReadAnalysisFrames* mtraj = plumed.getActionSet().selectWithLabel<ReadAnalysisFrames*>( mytraj );
if( !mtraj ) error(mytraj + " is not the label of a READ_ANALYSIS_FRAMES object");
- mydata = dynamic_cast<AnalysisBase*>( mtraj );
+ mydata = dynamic_cast<AnalysisBase*>( mtraj ); mydata->use_all_data=true;
}
if( mytraj.length()>0 && plumed.getActionSet().size()!=1 ) error("should only be this action and the READ_ANALYSIS_FRAMES command in the input file");
@@ -147,12 +148,6 @@ ReferenceConfiguration* ReadDissimilarityMatrix::getReferenceConfiguration( cons
return NULL;
}
-ReferenceConfiguration* ReadDissimilarityMatrix::getInputReferenceConfiguration( const unsigned& idata ){
- if( mydata ) return AnalysisBase::getInputReferenceConfiguration( idata );
- plumed_merror("cannot get reference configurations from read in dissimilarity matrix");
- return NULL;
-}
-
void ReadDissimilarityMatrix::getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const {
if( mydata ){ AnalysisBase::getDataPoint( idata, point, weight ); return; }
plumed_merror("cannot get data points from read in dissmimilarity matrix");
diff --git a/src/dimred/DimensionalityReductionBase.cpp b/src/dimred/DimensionalityReductionBase.cpp
index 364695734..aee9e3424 100644
--- a/src/dimred/DimensionalityReductionBase.cpp
+++ b/src/dimred/DimensionalityReductionBase.cpp
@@ -53,15 +53,11 @@ dimredbase(NULL)
}
ReferenceConfiguration* DimensionalityReductionBase::getReferenceConfiguration( const unsigned& idat ){
- ReferenceConfiguration* myref = mydata->getInputReferenceConfiguration( idat ); std::string num; myref->clearAllProperties();
+ ReferenceConfiguration* myref = mydata->getReferenceConfiguration( idat ); std::string num; myref->clearAllProperties();
for(unsigned i=0;i<nlow;++i){ Tools::convert(i+1,num); myref->attachProperty( getLabel() + "." + num, projections(idat,i) ); }
return myref;
}
-ReferenceConfiguration* DimensionalityReductionBase::getInputReferenceConfiguration( const unsigned& idat ){
- return mydata->getInputReferenceConfiguration( idat );
-}
-
void DimensionalityReductionBase::getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const {
if( point.size()!=nlow ) point.resize( nlow );
weight = getWeight(idata); for(unsigned i=0;i<nlow;++i) point[i]=projections(idata,i);
diff --git a/src/dimred/DimensionalityReductionBase.h b/src/dimred/DimensionalityReductionBase.h
index e06be9d81..49fee7c3d 100644
--- a/src/dimred/DimensionalityReductionBase.h
+++ b/src/dimred/DimensionalityReductionBase.h
@@ -48,7 +48,6 @@ public:
void getDataPoint( const unsigned& idata, std::vector<double>& point, double& weight ) const ;
/// Get a reference configuration (this returns the projection)
ReferenceConfiguration* getReferenceConfiguration( const unsigned& idata );
- ReferenceConfiguration* getInputReferenceConfiguration( const unsigned& idata );
/// Actually perform the analysis
void performAnalysis();
/// Calculate the projections of points
diff --git a/src/dimred/ProjectNonLandmarkPoints.cpp b/src/dimred/ProjectNonLandmarkPoints.cpp
index 0dc28f101..7838a8880 100644
--- a/src/dimred/ProjectNonLandmarkPoints.cpp
+++ b/src/dimred/ProjectNonLandmarkPoints.cpp
@@ -57,7 +57,6 @@ public:
void getDataPoint( const unsigned& idat, std::vector<double>& point );
/// Get a reference configuration (this returns the projection)
ReferenceConfiguration* getReferenceConfiguration( const unsigned& idat );
- ReferenceConfiguration* getInputReferenceConfiguration( const unsigned& idat );
/// This does nothing -- projections are calculated when getDataPoint and getReferenceConfiguration are called
void performAnalysis(){}
/// This just calls calculate stress in the underlying projection object
@@ -107,15 +106,11 @@ void ProjectNonLandmarkPoints::generateProjection( const unsigned& idat, std::ve
ReferenceConfiguration* ProjectNonLandmarkPoints::getReferenceConfiguration( const unsigned& idat ){
std::vector<double> pp(nlow); generateProjection( idat, pp ); std::string num;
- ReferenceConfiguration* myref = mydata->getInputReferenceConfiguration( idat ); myref->clearAllProperties();
+ ReferenceConfiguration* myref = mydata->getReferenceConfiguration( idat ); myref->clearAllProperties();
for(unsigned i=0;i<nlow;++i){ Tools::convert(i+1,num); myref->attachProperty( getLabel() + "." + num, pp[i] ); }
return myref;
}
-ReferenceConfiguration* ProjectNonLandmarkPoints::getInputReferenceConfiguration( const unsigned& idat ){
- return mydata->getInputReferenceConfiguration( idat );
-}
-
void ProjectNonLandmarkPoints::getDataPoint( const unsigned& idat, std::vector<double>& point ){
if( point.size()!=nlow ) point.resize( nlow );
generateProjection( idat, point );
diff --git a/src/dimred/SketchMapBase.cpp b/src/dimred/SketchMapBase.cpp
index 81fda99b5..53eb8781e 100644
--- a/src/dimred/SketchMapBase.cpp
+++ b/src/dimred/SketchMapBase.cpp
@@ -90,7 +90,7 @@ void SketchMapBase::calculateProjections( const Matrix<double>& targets, Matrix<
}
}
// And minimse
- minimise( transformed, distances, projections );
+ minimise( projections );
}
double SketchMapBase::calculateStress( const std::vector<double>& p, std::vector<double>& d ){
diff --git a/src/dimred/SketchMapBase.h b/src/dimred/SketchMapBase.h
index 0095da93c..e4e99385b 100644
--- a/src/dimred/SketchMapBase.h
+++ b/src/dimred/SketchMapBase.h
@@ -37,12 +37,12 @@ private:
SketchMapBase* smapbase;
/// Switching functions for low and high dimensional space
SwitchingFunction lowdf, highdf;
-/// This holds the target distances and target transformed distances
- Matrix<double> distances, transformed;
/// This is used within calculate stress to hold the target distances and the
/// target values for the high dimensional switching function
std::vector<double> dtargets, ftargets;
protected:
+/// This holds the target distances and target transformed distances
+ Matrix<double> distances, transformed;
/// The fraction of pure distances to mix in when optimising
double mixparam;
public:
@@ -51,7 +51,7 @@ public:
/// This starts the process of calculating the projections
void calculateProjections( const Matrix<double>& , Matrix<double>& );
/// This finishes the process of calculating the prjections
- virtual void minimise( const Matrix<double>& , const Matrix<double>& , Matrix<double>& )=0;
+ virtual void minimise( Matrix<double>& )=0;
/// Apply the low dimensional switching function to the value val
double transformLowDimensionalDistance( const double& val, double& df ) const ;
/// Apply the high dimensional switching function to the value val
diff --git a/src/dimred/SketchMapPointwise.cpp b/src/dimred/SketchMapPointwise.cpp
index 21378ab09..bb1683665 100644
--- a/src/dimred/SketchMapPointwise.cpp
+++ b/src/dimred/SketchMapPointwise.cpp
@@ -45,7 +45,7 @@ private:
public:
static void registerKeywords( Keywords& keys );
SketchMapPointwise( const ActionOptions& ao );
- void minimise( const Matrix<double>& , const Matrix<double>& , Matrix<double>& );
+ void minimise( Matrix<double>& );
/// This is used in pointwise global optimization
double calculateFullStress( const std::vector<double>& p, std::vector<double>& d );
};
@@ -79,7 +79,7 @@ npoints(nlow)
if( nointerpolation ) log.printf(" not using any interpolation in grid search\n");
}
-void SketchMapPointwise::minimise( const Matrix<double>& transformed, const Matrix<double>& distances, Matrix<double>& projections ){
+void SketchMapPointwise::minimise( Matrix<double>& projections ){
std::vector<double> gmin( nlow ), gmax( nlow ), mypoint( nlow );
// Find the extent of the grid
@@ -118,51 +118,12 @@ void SketchMapPointwise::minimise( const Matrix<double>& transformed, const Matr
}
}
-void SketchMapPointwise::minimise( const Matrix<double>& transformed, const Matrix<double>& distances, Matrix<double>& projections ){
- std::vector<double> gmin( nlow ), gmax( nlow ), mypoint( nlow );
-
- // Find the extent of the grid
- for(unsigned j=0;j<nlow;++j) gmin[j]=gmax[j]=projections(0,j);
- for(unsigned i=1;i<getNumberOfDataPoints();++i){
- for(unsigned j=0;j<nlow;++j){
- if( projections(i,j) < gmin[j] ) gmin[j] = projections(i,j);
- if( projections(i,j) > gmax[j] ) gmax[j] = projections(i,j);
- }
- }
- for(unsigned j=0;j<nlow;++j){
- double gbuffer = 0.5*gbuf*( gmax[j]-gmin[j] ) - 0.5*( gmax[j]- gmin[j] );
- gmin[j]-=gbuffer; gmax[j]+=gbuffer;
- }
-
- // And do the search
- ConjugateGradient<SketchMapPointwise> mycgminimise( this );
- GridSearch<SketchMapPointwise> mygridsearch( gmin, gmax, npoints, this );
- // Run multiple loops over all projections
- for(unsigned i=0;i<ncycles;++i){
- for(unsigned j=0;j<getNumberOfDataPoints();++j){
- // Setup target distances and target functions for calculate stress
- for(unsigned k=0;k<getNumberOfDataPoints();++k) setTargetDistance( k, distances(j,k) );
-
- if( nointerpolation ){
- // Minimise using grid search
- mygridsearch.minimise( mypoint, &SketchMapPointwise::calculateStress );
- // Minimise output using conjugate gradient
- mycgminimise.minimise( cgtol, projections.getVector(), &SketchMapPointwise::calculateFullStress );
- } else {
- plumed_merror("use a class here that Sandip will implement that allows you to do this with some interpolation");
- }
- // Save new projection
- for(unsigned k=0;k<nlow;++k) projections(j,k)=mypoint[k];
- }
- }
-}
-
double SketchMapPointwise::calculateFullStress( const std::vector<double>& p, std::vector<double>& d ){
// Zero derivative and stress accumulators
for(unsigned i=0;i<p.size();++i) d[i]=0.0;
double stress=0; std::vector<double> dtmp( p.size() );
- for(unsigned i=1;i<dtargets.size();++i){
+ for(unsigned i=1;i<distances.nrows();++i){
for(unsigned j=0;j<i;++j){
// Calculate distance in low dimensional space
double dd=0;
diff --git a/src/dimred/SketchMapSmacof.cpp b/src/dimred/SketchMapSmacof.cpp
index cf0a7bf29..25f9c3d06 100644
--- a/src/dimred/SketchMapSmacof.cpp
+++ b/src/dimred/SketchMapSmacof.cpp
@@ -39,12 +39,11 @@ class SketchMapSmacof : public SketchMapBase {
private:
unsigned max_smap, maxiter;
double smap_tol, iter_tol, regulariser;
- double recalculateWeights( const Matrix<double>& transformed, const Matrix<double>& distances,
- const Matrix<double>& projections, Matrix<double>& weights );
+ double recalculateWeights( const Matrix<double>& projections, Matrix<double>& weights );
public:
static void registerKeywords( Keywords& keys );
SketchMapSmacof( const ActionOptions& ao );
- void minimise( const Matrix<double>& , const Matrix<double>& , Matrix<double>& );
+ void minimise( Matrix<double>& );
};
PLUMED_REGISTER_ACTION(SketchMapSmacof,"SKETCHMAP_SMACOF")
@@ -67,14 +66,14 @@ SketchMapBase(ao)
parse("SMACOF_TOL",smap_tol); parse("SMAP_TOL",iter_tol);
}
-void SketchMapSmacof::minimise( const Matrix<double>& transformed, const Matrix<double>& distances, Matrix<double>& projections ){
+void SketchMapSmacof::minimise( Matrix<double>& projections ){
Matrix<double> weights( distances.nrows(), distances.ncols() ); weights=0.;
- double filt = recalculateWeights( transformed, distances, projections, weights );
+ double filt = recalculateWeights( projections, weights );
for(unsigned i=0;i<maxiter;++i){
SMACOF::run( weights, distances, smap_tol, max_smap, projections );
// Recalculate weights matrix and sigma
- double newsig = recalculateWeights( transformed, distances, projections, weights );
+ double newsig = recalculateWeights( projections, weights );
printf("HELLO SMACOF %d %f %f \n",i,newsig,filt);
// Test whether or not the algorithm has converged
if( fabs( newsig - filt )<iter_tol ) break;
@@ -83,8 +82,7 @@ void SketchMapSmacof::minimise( const Matrix<double>& transformed, const Matrix<
}
}
-double SketchMapSmacof::recalculateWeights( const Matrix<double>& transformed, const Matrix<double>& distances,
- const Matrix<double>& projections, Matrix<double>& weights ){
+double SketchMapSmacof::recalculateWeights( const Matrix<double>& projections, Matrix<double>& weights ){
double filt=0, totalWeight=0.;; double dr;
for(unsigned i=1; i<weights.nrows(); ++i){
for(unsigned j=0; j<i; ++j){
diff --git a/src/reference/MultiDomainRMSD.cpp b/src/reference/MultiDomainRMSD.cpp
index b9e1eca5b..f802daa7f 100644
--- a/src/reference/MultiDomainRMSD.cpp
+++ b/src/reference/MultiDomainRMSD.cpp
@@ -52,6 +52,7 @@ void MultiDomainRMSD::read( const PDB& pdb ){
parse("LOWER_CUTOFF",lower,true);
parse("UPPER_CUTOFF",upper,true);
+ domains.resize(0); weights.resize(0);
for(unsigned i=1;i<=nblocks;++i){
Tools::convert(i,num);
if( ftype=="RMSD" ){
@@ -79,6 +80,7 @@ void MultiDomainRMSD::read( const PDB& pdb ){
else weights.push_back( ww );
}
// And set the atom numbers for this object
+ indices.resize(0); der_index.resize(0);
for(unsigned i=0;i<pdb.size();++i){ indices.push_back( pdb.getAtomNumbers()[i] ); der_index.push_back(i); }
// setAtomNumbers( pdb.getAtomNumbers() );
}
diff --git a/src/reference/OptimalRMSD.cpp b/src/reference/OptimalRMSD.cpp
index c4f08c962..012ff44b0 100644
--- a/src/reference/OptimalRMSD.cpp
+++ b/src/reference/OptimalRMSD.cpp
@@ -55,7 +55,7 @@ RMSDBase(ro)
}
void OptimalRMSD::read( const PDB& pdb ){
- readReference( pdb ); myrmsd.set(getAlign(),getDisplace(),getReferencePositions(),"OPTIMAL");
+ readReference( pdb ); myrmsd.clear(); myrmsd.set(getAlign(),getDisplace(),getReferencePositions(),"OPTIMAL");
}
double OptimalRMSD::calc( const std::vector<Vector>& pos, ReferenceValuePack& myder, const bool& squared ) const {
diff --git a/src/reference/ReferenceAtoms.cpp b/src/reference/ReferenceAtoms.cpp
index b97f2d4cb..48c4fbbad 100644
--- a/src/reference/ReferenceAtoms.cpp
+++ b/src/reference/ReferenceAtoms.cpp
@@ -34,6 +34,7 @@ checks_were_disabled(false)
void ReferenceAtoms::readAtomsFromPDB( const PDB& pdb ){
if( pdb.getNumberOfAtomBlocks()!=1 ) error("found multi-atom-block pdb format but expecting only one block of atoms");
+ indices.resize(0); reference_atoms.resize(0); align.resize(0); displace.resize(0); der_index.resize(0);
for(unsigned i=0;i<pdb.size();++i){
indices.push_back( pdb.getAtomNumbers()[i] ); reference_atoms.push_back( pdb.getPositions()[i] );
align.push_back( pdb.getOccupancy()[i] ); displace.push_back( pdb.getBeta()[i] ); der_index.push_back(i);
diff --git a/src/reference/ReferenceConfiguration.cpp b/src/reference/ReferenceConfiguration.cpp
index 892d0d206..5b91c3d0f 100644
--- a/src/reference/ReferenceConfiguration.cpp
+++ b/src/reference/ReferenceConfiguration.cpp
@@ -148,6 +148,14 @@ void ReferenceConfiguration::attachProperty( const std::string& name, const doub
if( !found ){ property_names.push_back( name ); property_values.push_back( val ); }
}
+double property_distance( ReferenceConfiguration* ref1, ReferenceConfiguration* ref2, const bool& squared ){
+ plumed_dbg_assert( ref1->property_values.size()>0 && ref2->propert_values.size()==ref1->property_values.size() );
+ unsigned nprop=ref1->property_values.size(); double dist=0;
+ for(unsigned i=0;i<nprop;++i){ double tmp=ref1->property_values[i]-ref2->property_values[i]; dist+=tmp*tmp; }
+ if(squared) return dist;
+ return sqrt(dist);
+}
+
double distance( const Pbc& pbc, const std::vector<Value*> & vals, ReferenceConfiguration* ref1, ReferenceConfiguration* ref2, const bool& squared ){
unsigned nder;
if( ref1->getReferencePositions().size()>0 ) nder=ref1->getReferenceArguments().size() + 3*ref1->getReferencePositions().size() + 9;
diff --git a/src/reference/ReferenceConfiguration.h b/src/reference/ReferenceConfiguration.h
index a83e31f28..081d38e94 100644
--- a/src/reference/ReferenceConfiguration.h
+++ b/src/reference/ReferenceConfiguration.h
@@ -58,6 +58,7 @@ public:
class ReferenceConfiguration {
friend class SingleDomainRMSD;
+friend double property_distance( ReferenceConfiguration* ref1, ReferenceConfiguration* ref2, const bool& squared );
friend double distance( const Pbc& pbc, const std::vector<Value*> & vals, ReferenceConfiguration*, ReferenceConfiguration*, const bool& squared );
private:
/// The name of this particular config
--
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