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Commit debe8341 authored by Gareth Tribello's avatar Gareth Tribello
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Moved collection of data for analysis to separate action 

Also tidied up how STRIDE and USE_ALL_DATA works for analysis
objects.  Now everything works in a manner similar to GRID
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regtest/analysis/rt-calc-dissims/analysis.0.mymatrix3.dat.reference
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View file @ debe8341
0.0000 1.0000 2.0000 3.0000 4.0000 5.0000 0.0000 0.0000 1.0000 2.0000 3.0000 4.0000
1.0000 0.0000 1.0000 2.0000 3.0000 4.0000 0.0000 0.0000 1.0000 2.0000 3.0000 4.0000
2.0000 1.0000 0.0000 1.0000 2.0000 3.0000 1.0000 1.0000 0.0000 1.0000 2.0000 3.0000
3.0000 2.0000 1.0000 0.0000 1.0000 2.0000 2.0000 2.0000 1.0000 0.0000 1.0000 2.0000
4.0000 3.0000 2.0000 1.0000 0.0000 1.0000 3.0000 3.0000 2.0000 1.0000 0.0000 1.0000
5.0000 4.0000 3.0000 2.0000 1.0000 0.0000 4.0000 4.0000 3.0000 2.0000 1.0000 0.0000
regtest/analysis/rt-calc-dissims/colv_in
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#! FIELDS time data #! FIELDS time data
0 10
0 0 0 0
1 0 1 0
2 1 2 1
......
regtest/analysis/rt-calc-dissims/output-fps.pdb.reference
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View file @ debe8341
DESCRIPTION: analysis data from calculation done by @8 at time 12.000000 DESCRIPTION: analysis data from calculation done by @9 at time 13.000000
REMARK TYPE=EUCLIDEAN
REMARK WEIGHT=6.000000 REMARK WEIGHT=6.000000
REMARK TYPE=EUCLIDEAN
REMARK ARG=d1 REMARK ARG=d1
REMARK d1=7.000000 REMARK d1=7.000000
END END
DESCRIPTION: analysis data from calculation done by @8 at time 12.000000 DESCRIPTION: analysis data from calculation done by @9 at time 13.000000
REMARK TYPE=EUCLIDEAN
REMARK WEIGHT=5.000000 REMARK WEIGHT=5.000000
REMARK TYPE=EUCLIDEAN
REMARK ARG=d1 REMARK ARG=d1
REMARK d1=0.000000 REMARK d1=0.000000
END END
DESCRIPTION: analysis data from calculation done by @8 at time 12.000000 DESCRIPTION: analysis data from calculation done by @9 at time 13.000000
REMARK TYPE=EUCLIDEAN
REMARK WEIGHT=2.000000 REMARK WEIGHT=2.000000
REMARK TYPE=EUCLIDEAN
REMARK ARG=d1 REMARK ARG=d1
REMARK d1=11.000000 REMARK d1=11.000000
END END
regtest/analysis/rt-calc-dissims/output-stride.pdb.reference
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View file @ debe8341
DESCRIPTION: analysis data from calculation done by @5 at time 12.000000 DESCRIPTION: analysis data from calculation done by @6 at time 13.000000
REMARK TYPE=EUCLIDEAN
REMARK WEIGHT=2.000000 REMARK WEIGHT=2.000000
REMARK TYPE=EUCLIDEAN
REMARK ARG=d1 REMARK ARG=d1
REMARK d1=0.000000 REMARK d1=0.000000
END END
DESCRIPTION: analysis data from calculation done by @5 at time 12.000000 DESCRIPTION: analysis data from calculation done by @6 at time 13.000000
REMARK TYPE=EUCLIDEAN
REMARK WEIGHT=2.000000 REMARK WEIGHT=2.000000
REMARK TYPE=EUCLIDEAN
REMARK ARG=d1 REMARK ARG=d1
REMARK d1=1.000000 REMARK d1=1.000000
END END
DESCRIPTION: analysis data from calculation done by @5 at time 12.000000 DESCRIPTION: analysis data from calculation done by @6 at time 13.000000
REMARK TYPE=EUCLIDEAN
REMARK WEIGHT=2.000000 REMARK WEIGHT=2.000000
REMARK TYPE=EUCLIDEAN
REMARK ARG=d1 REMARK ARG=d1
REMARK d1=3.000000 REMARK d1=3.000000
END END
DESCRIPTION: analysis data from calculation done by @5 at time 12.000000 DESCRIPTION: analysis data from calculation done by @6 at time 13.000000
REMARK TYPE=EUCLIDEAN
REMARK WEIGHT=2.000000 REMARK WEIGHT=2.000000
REMARK TYPE=EUCLIDEAN
REMARK ARG=d1 REMARK ARG=d1
REMARK d1=5.000000 REMARK d1=5.000000
END END
DESCRIPTION: analysis data from calculation done by @5 at time 12.000000 DESCRIPTION: analysis data from calculation done by @6 at time 13.000000
REMARK TYPE=EUCLIDEAN
REMARK WEIGHT=5.000000 REMARK WEIGHT=5.000000
REMARK TYPE=EUCLIDEAN
REMARK ARG=d1 REMARK ARG=d1
REMARK d1=7.000000 REMARK d1=7.000000
END END
regtest/analysis/rt-calc-dissims/plumed.dat
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d1: READ FILE=colv_in VALUES=data d1: READ FILE=colv_in VALUES=data
ss1: EUCLIDEAN_DISSIMILARITIES STRIDE=1 USE_ALL_DATA ARG=d1 ff: COLLECT_FRAMES ARG=d1 STRIDE=1
ss1: EUCLIDEAN_DISSIMILARITIES USE_OUTPUT_DATA_FROM=ff
PRINT_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=ss1 FILE=mymatrix.dat FMT=%8.4f PRINT_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=ss1 FILE=mymatrix.dat FMT=%8.4f
ll1: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=ss1 NLANDMARKS=5 ll1: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=ss1 NLANDMARKS=5
...@@ -11,5 +13,6 @@ PRINT_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=ll1 FILE=mymatrix2.dat FMT=%8.4f ...@@ -11,5 +13,6 @@ PRINT_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=ll1 FILE=mymatrix2.dat FMT=%8.4f
ll2: LANDMARK_SELECT_FPS USE_OUTPUT_DATA_FROM=ss1 NLANDMARKS=3 ll2: LANDMARK_SELECT_FPS USE_OUTPUT_DATA_FROM=ss1 NLANDMARKS=3
OUTPUT_ANALYSIS_DATA_TO_PDB USE_OUTPUT_DATA_FROM=ll2 FILE=output-fps.pdb OUTPUT_ANALYSIS_DATA_TO_PDB USE_OUTPUT_DATA_FROM=ll2 FILE=output-fps.pdb
ss3: EUCLIDEAN_DISSIMILARITIES STRIDE=1 RUN=6 ARG=d1 ff2: COLLECT_FRAMES ARG=d1 CLEAR=6 STRIDE=1
oo: PRINT_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=ss3 FILE=mymatrix3.dat FMT=%8.4f ss3: EUCLIDEAN_DISSIMILARITIES USE_OUTPUT_DATA_FROM=ff2
oo: PRINT_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=ss3 FILE=mymatrix3.dat STRIDE=6 FMT=%8.4f
regtest/analysis/rt-calc-dissims2/config
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type=driver type=driver
# this is to test a different name # 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" arg="--plumed plumed.dat --ixyz traj.xyz"
extra_files="../../trajectories/trajectory.xyz" extra_files="../rt-read-dissims2/traj.xyz"
regtest/analysis/rt-calc-dissims2/configs-stride.pdb.reference
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View file @ debe8341
DESCRIPTION: analysis data from calculation done by @5 at time 0.200000 DESCRIPTION: analysis data from calculation done by @5 at time 5.000000
REMARK TYPE=EUCLIDEAN
REMARK WEIGHT=1.0000 REMARK WEIGHT=1.0000
REMARK TYPE=OPTIMAL REMARK ARG=d1,d2
ATOM 1 X RES 0 -4.506 -11.060 -17.545 0.05 0.05 REMARK d1=1.2626 d2=1.0972
ATOM 2 X RES 1 4.963 -11.182 -9.194 0.05 0.05 ATOM 1 X RES 0 -0.344 -0.030 0.090 1.00 1.00
ATOM 3 X RES 2 4.162 -2.540 -17.207 0.05 0.05 ATOM 2 X RES 1 9.125 -0.152 8.441 1.00 1.00
ATOM 4 X RES 3 -3.809 -2.069 -9.681 0.05 0.05 ATOM 3 X RES 2 8.323 8.489 0.428 1.00 1.00
ATOM 5 X RES 4 -4.180 -10.584 -1.418 0.05 0.05 ATOM 4 X RES 3 0.353 8.960 7.953 1.00 1.00
ATOM 6 X RES 5 4.447 -10.620 7.264 0.05 0.05 ATOM 5 X RES 4 -0.019 0.445 16.216 1.00 1.00
ATOM 7 X RES 6 4.385 -2.599 -0.952 0.05 0.05 ATOM 6 X RES 5 8.609 0.409 24.898 1.00 1.00
ATOM 8 X RES 7 -4.264 -2.879 7.660 0.05 0.05 ATOM 7 X RES 6 8.547 8.430 16.683 1.00 1.00
ATOM 9 X RES 8 -5.027 -10.867 15.899 0.05 0.05 ATOM 8 X RES 7 -0.103 8.150 25.295 1.00 1.00
ATOM 10 X RES 9 3.620 -10.890 24.529 0.05 0.05 ATOM 9 X RES 8 -0.866 0.162 33.533 1.00 1.00
ATOM 11 X RES 10 4.490 -2.292 15.828 0.05 0.05 ATOM 10 X RES 9 7.781 0.139 42.164 1.00 1.00
ATOM 12 X RES 11 -4.496 -2.174 24.340 0.05 0.05 ATOM 11 X RES 10 8.652 8.737 33.463 1.00 1.00
ATOM 13 X RES 12 -3.720 5.418 -17.405 0.05 0.05 ATOM 12 X RES 11 -0.335 8.856 41.975 1.00 1.00
ATOM 14 X RES 13 3.623 5.966 -9.542 0.05 0.05 ATOM 13 X RES 12 0.441 16.447 0.229 1.00 1.00
ATOM 15 X RES 14 4.401 14.249 -18.015 0.05 0.05 ATOM 14 X RES 13 7.784 16.995 8.093 1.00 1.00
ATOM 16 X RES 15 -3.820 14.172 -9.591 0.05 0.05 ATOM 15 X RES 14 8.562 25.278 -0.380 1.00 1.00
ATOM 17 X RES 16 -4.504 5.758 -0.036 0.05 0.05 ATOM 16 X RES 15 0.341 25.201 8.043 1.00 1.00
ATOM 18 X RES 17 3.305 5.096 7.190 0.05 0.05 ATOM 17 X RES 16 -0.343 16.787 17.598 1.00 1.00
ATOM 19 X RES 18 4.331 14.345 0.009 0.05 0.05 ATOM 18 X RES 17 7.466 16.126 24.825 1.00 1.00
ATOM 20 X RES 19 -3.402 14.752 7.866 0.05 0.05 ATOM 19 X RES 18 8.493 25.374 17.644 1.00 1.00
ATOM 20 X RES 19 0.760 25.782 25.501 1.00 1.00
END END
DESCRIPTION: analysis data from calculation done by @5 at time 0.200000 DESCRIPTION: analysis data from calculation done by @5 at time 5.000000
REMARK TYPE=EUCLIDEAN
REMARK WEIGHT=1.0000 REMARK WEIGHT=1.0000
REMARK TYPE=OPTIMAL REMARK ARG=d1,d2
ATOM 1 X RES 0 -4.670 -11.130 -17.511 0.05 0.05 REMARK d1=1.3176 d2=1.0588
ATOM 2 X RES 1 5.583 -11.209 -9.235 0.05 0.05 ATOM 1 X RES 0 -0.551 -0.033 0.122 1.00 1.00
ATOM 3 X RES 2 4.301 -2.482 -16.840 0.05 0.05 ATOM 2 X RES 1 9.701 -0.112 8.398 1.00 1.00
ATOM 4 X RES 3 -3.760 -1.929 -9.998 0.05 0.05 ATOM 3 X RES 2 8.420 8.616 0.793 1.00 1.00
ATOM 5 X RES 4 -4.201 -10.212 -1.856 0.05 0.05 ATOM 4 X RES 3 0.359 9.168 7.635 1.00 1.00
ATOM 6 X RES 5 4.506 -10.293 7.185 0.05 0.05 ATOM 5 X RES 4 -0.082 0.885 15.777 1.00 1.00
ATOM 7 X RES 6 4.647 -2.750 -1.114 0.05 0.05 ATOM 6 X RES 5 8.625 0.805 24.817 1.00 1.00
ATOM 8 X RES 7 -4.477 -3.337 7.694 0.05 0.05 ATOM 7 X RES 6 8.766 8.348 16.519 1.00 1.00
ATOM 9 X RES 8 -5.755 -10.773 16.018 0.05 0.05 ATOM 8 X RES 7 -0.359 7.760 25.327 1.00 1.00
ATOM 10 X RES 9 3.124 -11.030 24.688 0.05 0.05 ATOM 9 X RES 8 -1.636 0.324 33.650 1.00 1.00
ATOM 11 X RES 10 4.814 -2.000 15.677 0.05 0.05 ATOM 10 X RES 9 7.243 0.067 42.321 1.00 1.00
ATOM 12 X RES 11 -4.491 -1.806 24.342 0.05 0.05 ATOM 11 X RES 10 8.933 9.098 33.309 1.00 1.00
ATOM 13 X RES 12 -3.379 5.315 -17.527 0.05 0.05 ATOM 12 X RES 11 -0.372 9.291 41.974 1.00 1.00
ATOM 14 X RES 13 3.257 6.072 -9.818 0.05 0.05 ATOM 13 X RES 12 0.739 16.412 0.106 1.00 1.00
ATOM 15 X RES 14 4.689 14.018 -18.419 0.05 0.05 ATOM 14 X RES 13 7.375 17.169 7.815 1.00 1.00
ATOM 16 X RES 15 -3.518 14.143 -9.834 0.05 0.05 ATOM 15 X RES 14 8.808 25.116 -0.786 1.00 1.00
ATOM 17 X RES 16 -4.862 5.640 0.653 0.05 0.05 ATOM 16 X RES 15 0.601 25.241 7.799 1.00 1.00
ATOM 18 X RES 17 2.779 4.548 6.887 0.05 0.05 ATOM 17 X RES 16 -0.743 16.737 18.286 1.00 1.00
ATOM 19 X RES 18 4.460 14.224 0.649 0.05 0.05 ATOM 18 X RES 17 6.898 15.646 24.519 1.00 1.00
ATOM 20 X RES 19 -3.049 14.991 8.360 0.05 0.05 ATOM 19 X RES 18 8.578 25.322 18.282 1.00 1.00
ATOM 20 X RES 19 1.070 26.089 25.993 1.00 1.00
END END
DESCRIPTION: analysis data from calculation done by @5 at time 0.200000 DESCRIPTION: analysis data from calculation done by @5 at time 5.000000
REMARK TYPE=EUCLIDEAN
REMARK WEIGHT=1.0000 REMARK WEIGHT=1.0000
REMARK TYPE=OPTIMAL REMARK ARG=d1,d2
ATOM 1 X RES 0 -4.797 -10.892 -17.524 0.05 0.05 REMARK d1=1.3934 d2=1.0958
ATOM 2 X RES 1 6.238 -10.978 -9.016 0.05 0.05 ATOM 1 X RES 0 -0.728 0.172 0.094 1.00 1.00
ATOM 3 X RES 2 4.510 -2.450 -16.757 0.05 0.05 ATOM 2 X RES 1 10.307 0.085 8.601 1.00 1.00
ATOM 4 X RES 3 -4.186 -2.197 -10.094 0.05 0.05 ATOM 3 X RES 2 8.579 8.613 0.861 1.00 1.00
ATOM 5 X RES 4 -4.154 -9.504 -2.049 0.05 0.05 ATOM 4 X RES 3 -0.117 8.867 7.523 1.00 1.00
ATOM 6 X RES 5 4.557 -9.886 7.278 0.05 0.05 ATOM 5 X RES 4 -0.086 1.559 15.568 1.00 1.00
ATOM 7 X RES 6 4.879 -2.888 -1.227 0.05 0.05 ATOM 6 X RES 5 8.626 1.178 24.895 1.00 1.00
ATOM 8 X RES 7 -4.895 -3.556 7.522 0.05 0.05 ATOM 7 X RES 6 8.947 8.175 16.391 1.00 1.00
ATOM 9 X RES 8 -6.393 -11.011 16.310 0.05 0.05 ATOM 8 X RES 7 -0.826 7.508 25.139 1.00 1.00
ATOM 10 X RES 9 2.498 -11.182 24.664 0.05 0.05 ATOM 9 X RES 8 -2.324 0.053 33.927 1.00 1.00
ATOM 11 X RES 10 5.288 -1.860 15.693 0.05 0.05 ATOM 10 X RES 9 6.566 -0.118 42.281 1.00 1.00
ATOM 12 X RES 11 -3.861 -1.562 24.588 0.05 0.05 ATOM 11 X RES 10 9.356 9.203 33.310 1.00 1.00
ATOM 13 X RES 12 -3.013 5.578 -18.094 0.05 0.05 ATOM 12 X RES 11 0.208 9.501 42.205 1.00 1.00
ATOM 14 X RES 13 3.214 6.210 -9.768 0.05 0.05 ATOM 13 X RES 12 1.056 16.641 -0.477 1.00 1.00
ATOM 15 X RES 14 5.034 13.706 -18.661 0.05 0.05 ATOM 14 X RES 13 7.283 17.274 7.849 1.00 1.00
ATOM 16 X RES 15 -3.380 14.173 -10.000 0.05 0.05 ATOM 15 X RES 14 9.103 24.770 -1.044 1.00 1.00
ATOM 17 X RES 16 -5.496 5.677 0.663 0.05 0.05 ATOM 16 X RES 15 0.688 25.236 7.617 1.00 1.00
ATOM 18 X RES 17 2.962 4.118 6.770 0.05 0.05 ATOM 17 X RES 16 -1.428 16.741 18.280 1.00 1.00
ATOM 19 X RES 18 4.381 13.795 0.873 0.05 0.05 ATOM 18 X RES 17 7.031 15.181 24.387 1.00 1.00
ATOM 20 X RES 19 -3.386 14.709 8.831 0.05 0.05 ATOM 19 X RES 18 8.450 24.859 18.490 1.00 1.00
ATOM 20 X RES 19 0.682 25.773 26.448 1.00 1.00
END END
DESCRIPTION: analysis data from calculation done by @5 at time 0.200000 DESCRIPTION: analysis data from calculation done by @5 at time 5.000000
REMARK TYPE=EUCLIDEAN
REMARK WEIGHT=1.0000 REMARK WEIGHT=1.0000
REMARK TYPE=OPTIMAL REMARK ARG=d1,d2
ATOM 1 X RES 0 -4.972 -10.651 -17.468 0.05 0.05 REMARK d1=1.4755 d2=1.1628
ATOM 2 X RES 1 6.834 -10.601 -8.619 0.05 0.05 ATOM 1 X RES 0 -0.874 0.351 0.130 1.00 1.00
ATOM 3 X RES 2 4.839 -2.454 -16.913 0.05 0.05 ATOM 2 X RES 1 10.933 0.401 8.979 1.00 1.00
ATOM 4 X RES 3 -4.685 -2.410 -10.241 0.05 0.05 ATOM 3 X RES 2 8.938 8.548 0.685 1.00 1.00
ATOM 5 X RES 4 -4.184 -8.718 -1.928 0.05 0.05 ATOM 4 X RES 3 -0.586 8.592 7.357 1.00 1.00
ATOM 6 X RES 5 4.622 -9.418 7.529 0.05 0.05 ATOM 5 X RES 4 -0.086 2.284 15.670 1.00 1.00
ATOM 7 X RES 6 5.110 -2.972 -1.473 0.05 0.05 ATOM 6 X RES 5 8.720 1.584 25.127 1.00 1.00
ATOM 8 X RES 7 -5.319 -3.420 7.484 0.05 0.05 ATOM 7 X RES 6 9.208 8.030 16.125 1.00 1.00
ATOM 9 X RES 8 -7.099 -11.271 16.457 0.05 0.05 ATOM 8 X RES 7 -1.221 7.582 25.082 1.00 1.00
ATOM 10 X RES 9 1.795 -11.424 24.536 0.05 0.05 ATOM 9 X RES 8 -3.001 -0.269 34.055 1.00 1.00
ATOM 11 X RES 10 6.011 -2.234 15.660 0.05 0.05 ATOM 10 X RES 9 5.894 -0.422 42.134 1.00 1.00
ATOM 12 X RES 11 -3.246 -1.671 24.754 0.05 0.05 ATOM 11 X RES 10 10.110 8.768 33.258 1.00 1.00
ATOM 13 X RES 12 -2.534 5.845 -18.557 0.05 0.05 ATOM 12 X RES 11 0.852 9.331 42.351 1.00 1.00
ATOM 14 X RES 13 3.368 6.364 -9.489 0.05 0.05 ATOM 13 X RES 12 1.565 16.847 -0.959 1.00 1.00
ATOM 15 X RES 14 5.174 13.639 -18.574 0.05 0.05 ATOM 14 X RES 13 7.466 17.366 8.108 1.00 1.00
ATOM 16 X RES 15 -3.367 14.132 -10.036 0.05 0.05 ATOM 15 X RES 14 9.273 24.641 -0.976 1.00 1.00
ATOM 17 X RES 16 -6.083 5.704 0.149 0.05 0.05 ATOM 16 X RES 15 0.732 25.134 7.562 1.00 1.00
ATOM 18 X RES 17 3.390 3.801 6.837 0.05 0.05 ATOM 17 X RES 16 -1.984 16.706 17.747 1.00 1.00
ATOM 19 X RES 18 4.216 13.533 0.747 0.05 0.05 ATOM 18 X RES 17 7.489 14.803 24.434 1.00 1.00
ATOM 20 X RES 19 -3.871 14.225 9.145 0.05 0.05 ATOM 19 X RES 18 8.315 24.535 18.345 1.00 1.00
ATOM 20 X RES 19 0.228 25.227 26.742 1.00 1.00
END END
DESCRIPTION: analysis data from calculation done by @5 at time 0.200000 DESCRIPTION: analysis data from calculation done by @5 at time 5.000000
REMARK TYPE=EUCLIDEAN
REMARK WEIGHT=1.0000 REMARK WEIGHT=1.0000
REMARK TYPE=OPTIMAL REMARK ARG=d1,d2
ATOM 1 X RES 0 -5.103 -10.424 -17.164 0.05 0.05 REMARK d1=1.4908 d2=1.2160
ATOM 2 X RES 1 7.050 -10.389 -8.531 0.05 0.05 ATOM 1 X RES 0 -0.914 0.528 0.408 1.00 1.00
ATOM 3 X RES 2 5.143 -2.344 -17.090 0.05 0.05 ATOM 2 X RES 1 11.239 0.563 9.041 1.00 1.00
ATOM 4 X RES 3 -5.107 -2.193 -10.548 0.05 0.05 ATOM 3 X RES 2 9.332 8.608 0.482 1.00 1.00
ATOM 5 X RES 4 -4.327 -8.390 -1.659 0.05 0.05 ATOM 4 X RES 3 -0.918 8.759 7.023 1.00 1.00
ATOM 6 X RES 5 4.658 -8.831 7.681 0.05 0.05 ATOM 5 X RES 4 -0.138 2.562 15.913 1.00 1.00
ATOM 7 X RES 6 5.148 -2.700 -1.836 0.05 0.05 ATOM 6 X RES 5 8.848 2.121 25.253 1.00 1.00
ATOM 8 X RES 7 -5.562 -2.969 7.578 0.05 0.05 ATOM 7 X RES 6 9.337 8.252 15.736 1.00 1.00
ATOM 9 X RES 8 -7.494 -11.552 16.355 0.05 0.05 ATOM 8 X RES 7 -1.372 7.983 25.150 1.00 1.00
ATOM 10 X RES 9 1.117 -11.563 24.384 0.05 0.05 ATOM 9 X RES 8 -3.304 -0.600 33.927 1.00 1.00
ATOM 11 X RES 10 6.514 -2.686 15.870 0.05 0.05 ATOM 10 X RES 9 5.306 -0.610 41.956 1.00 1.00
ATOM 12 X RES 11 -2.790 -2.003 24.821 0.05 0.05 ATOM 11 X RES 10 10.704 8.266 33.441 1.00 1.00
ATOM 13 X RES 12 -1.938 5.998 -18.490 0.05 0.05 ATOM 12 X RES 11 1.399 8.949 42.393 1.00 1.00
ATOM 14 X RES 13 3.749 6.279 -9.026 0.05 0.05 ATOM 13 X RES 12 2.252 16.950 -0.918 1.00 1.00
ATOM 15 X RES 14 5.216 13.612 -18.212 0.05 0.05 ATOM 14 X RES 13 7.938 17.231 8.546 1.00 1.00
ATOM 16 X RES 15 -3.250 14.142 -9.905 0.05 0.05 ATOM 15 X RES 14 9.405 24.564 -0.640 1.00 1.00
ATOM 17 X RES 16 -6.457 5.381 -0.665 0.05 0.05 ATOM 16 X RES 15 0.939 25.094 7.667 1.00 1.00
ATOM 18 X RES 17 3.858 3.517 6.807 0.05 0.05 ATOM 17 X RES 16 -2.267 16.333 16.907 1.00 1.00
ATOM 19 X RES 18 3.999 13.370 0.561 0.05 0.05 ATOM 18 X RES 17 8.048 14.469 24.379 1.00 1.00
ATOM 20 X RES 19 -4.422 13.745 9.068 0.05 0.05 ATOM 19 X RES 18 8.189 24.322 18.133 1.00 1.00
ATOM 20 X RES 19 -0.233 24.697 26.640 1.00 1.00
END END
regtest/analysis/rt-calc-dissims2/plumed.dat
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d1: DISTANCE ATOMS=1,2 d1: DISTANCE ATOMS=1,2
d2: DISTANCE ATOMS=3,4 d2: DISTANCE ATOMS=3,4
c1: COLLECT_FRAMES ATOMS=1-20 STRIDE=1 USE_ALL_DATA c1: COLLECT_FRAMES ATOMS=1-20 ARG=d1,d2 STRIDE=1
r1: EUCLIDEAN_DISSIMILARITIES FRAMES=c1 ARG=d1,d2 r1: EUCLIDEAN_DISSIMILARITIES USE_OUTPUT_DATA_FROM=c1 ARG=d1,d2
l1: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=r1 NLANDMARKS=5 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 OUTPUT_ANALYSIS_DATA_TO_PDB USE_OUTPUT_DATA_FROM=l1 FILE=configs-stride.pdb FMT=%8.4f
regtest/analysis/rt-read-dissims2/config
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type=driver type=driver
# this is to test a different name # 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" arg="--plumed plumed.dat --ixyz traj.xyz"
extra_files="../../trajectories/trajectory.xyz"
regtest/analysis/rt-read-dissims2/configs-stride.pdb.reference
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View file @ debe8341
DESCRIPTION: analysis data from calculation done by @5 at time 0.200000 DESCRIPTION: analysis data from calculation done by @5 at time 5.000000
REMARK TYPE=UNKNOWN
REMARK WEIGHT=1.0000 REMARK WEIGHT=1.0000
REMARK TYPE=OPTIMAL ATOM 1 X RES 0 -0.344 -0.030 0.090 1.00 1.00
ATOM 1 X RES 0 -4.506 -11.060 -17.545 0.05 0.05 ATOM 2 X RES 1 9.125 -0.152 8.441 1.00 1.00
ATOM 2 X RES 1 4.963 -11.182 -9.194 0.05 0.05 ATOM 3 X RES 2 8.323 8.489 0.428 1.00 1.00
ATOM 3 X RES 2 4.162 -2.540 -17.207 0.05 0.05 ATOM 4 X RES 3 0.353 8.960 7.953 1.00 1.00
ATOM 4 X RES 3 -3.809 -2.069 -9.681 0.05 0.05 ATOM 5 X RES 4 -0.019 0.445 16.216 1.00 1.00
ATOM 5 X RES 4 -4.180 -10.584 -1.418 0.05 0.05 ATOM 6 X RES 5 8.609 0.409 24.898 1.00 1.00
ATOM 6 X RES 5 4.447 -10.620 7.264 0.05 0.05 ATOM 7 X RES 6 8.547 8.430 16.683 1.00 1.00
ATOM 7 X RES 6 4.385 -2.599 -0.952 0.05 0.05 ATOM 8 X RES 7 -0.103 8.150 25.295 1.00 1.00
ATOM 8 X RES 7 -4.264 -2.879 7.660 0.05 0.05 ATOM 9 X RES 8 -0.866 0.162 33.533 1.00 1.00
ATOM 9 X RES 8 -5.027 -10.867 15.899 0.05 0.05 ATOM 10 X RES 9 7.781 0.139 42.164 1.00 1.00
ATOM 10 X RES 9 3.620 -10.890 24.529 0.05 0.05 ATOM 11 X RES 10 8.652 8.737 33.463 1.00 1.00
ATOM 11 X RES 10 4.490 -2.292 15.828 0.05 0.05 ATOM 12 X RES 11 -0.335 8.856 41.975 1.00 1.00
ATOM 12 X RES 11 -4.496 -2.174 24.340 0.05 0.05 ATOM 13 X RES 12 0.441 16.447 0.229 1.00 1.00
ATOM 13 X RES 12 -3.720 5.418 -17.405 0.05 0.05 ATOM 14 X RES 13 7.784 16.995 8.093 1.00 1.00
ATOM 14 X RES 13 3.623 5.966 -9.542 0.05 0.05 ATOM 15 X RES 14 8.562 25.278 -0.380 1.00 1.00
ATOM 15 X RES 14 4.401 14.249 -18.015 0.05 0.05 ATOM 16 X RES 15 0.341 25.201 8.043 1.00 1.00
ATOM 16 X RES 15 -3.820 14.172 -9.591 0.05 0.05 ATOM 17 X RES 16 -0.343 16.787 17.598 1.00 1.00
ATOM 17 X RES 16 -4.504 5.758 -0.036 0.05 0.05 ATOM 18 X RES 17 7.466 16.126 24.825 1.00 1.00
ATOM 18 X RES 17 3.305 5.096 7.190 0.05 0.05 ATOM 19 X RES 18 8.493 25.374 17.644 1.00 1.00
ATOM 19 X RES 18 4.331 14.345 0.009 0.05 0.05 ATOM 20 X RES 19 0.760 25.782 25.501 1.00 1.00
ATOM 20 X RES 19 -3.402 14.752 7.866 0.05 0.05
END END
DESCRIPTION: analysis data from calculation done by @5 at time 0.200000 DESCRIPTION: analysis data from calculation done by @5 at time 5.000000
REMARK TYPE=UNKNOWN
REMARK WEIGHT=1.0000 REMARK WEIGHT=1.0000
REMARK TYPE=OPTIMAL ATOM 1 X RES 0 -0.551 -0.033 0.122 1.00 1.00
ATOM 1 X RES 0 -4.670 -11.130 -17.511 0.05 0.05 ATOM 2 X RES 1 9.701 -0.112 8.398 1.00 1.00
ATOM 2 X RES 1 5.583 -11.209 -9.235 0.05 0.05 ATOM 3 X RES 2 8.420 8.616 0.793 1.00 1.00
ATOM 3 X RES 2 4.301 -2.482 -16.840 0.05 0.05 ATOM 4 X RES 3 0.359 9.168 7.635 1.00 1.00
ATOM 4 X RES 3 -3.760 -1.929 -9.998 0.05 0.05 ATOM 5 X RES 4 -0.082 0.885 15.777 1.00 1.00
ATOM 5 X RES 4 -4.201 -10.212 -1.856 0.05 0.05 ATOM 6 X RES 5 8.625 0.805 24.817 1.00 1.00
ATOM 6 X RES 5 4.506 -10.293 7.185 0.05 0.05 ATOM 7 X RES 6 8.766 8.348 16.519 1.00 1.00
ATOM 7 X RES 6 4.647 -2.750 -1.114 0.05 0.05 ATOM 8 X RES 7 -0.359 7.760 25.327 1.00 1.00
ATOM 8 X RES 7 -4.477 -3.337 7.694 0.05 0.05 ATOM 9 X RES 8 -1.636 0.324 33.650 1.00 1.00
ATOM 9 X RES 8 -5.755 -10.773 16.018 0.05 0.05 ATOM 10 X RES 9 7.243 0.067 42.321 1.00 1.00
ATOM 10 X RES 9 3.124 -11.030 24.688 0.05 0.05 ATOM 11 X RES 10 8.933 9.098 33.309 1.00 1.00
ATOM 11 X RES 10 4.814 -2.000 15.677 0.05 0.05 ATOM 12 X RES 11 -0.372 9.291 41.974 1.00 1.00
ATOM 12 X RES 11 -4.491 -1.806 24.342 0.05 0.05 ATOM 13 X RES 12 0.739 16.412 0.106 1.00 1.00
ATOM 13 X RES 12 -3.379 5.315 -17.527 0.05 0.05 ATOM 14 X RES 13 7.375 17.169 7.815 1.00 1.00
ATOM 14 X RES 13 3.257 6.072 -9.818 0.05 0.05 ATOM 15 X RES 14 8.808 25.116 -0.786 1.00 1.00
ATOM 15 X RES 14 4.689 14.018 -18.419 0.05 0.05 ATOM 16 X RES 15 0.601 25.241 7.799 1.00 1.00
ATOM 16 X RES 15 -3.518 14.143 -9.834 0.05 0.05 ATOM 17 X RES 16 -0.743 16.737 18.286 1.00 1.00
ATOM 17 X RES 16 -4.862 5.640 0.653 0.05 0.05 ATOM 18 X RES 17 6.898 15.646 24.519 1.00 1.00
ATOM 18 X RES 17 2.779 4.548 6.887 0.05 0.05 ATOM 19 X RES 18 8.578 25.322 18.282 1.00 1.00
ATOM 19 X RES 18 4.460 14.224 0.649 0.05 0.05 ATOM 20 X RES 19 1.070 26.089 25.993 1.00 1.00
ATOM 20 X RES 19 -3.049 14.991 8.360 0.05 0.05
END END
DESCRIPTION: analysis data from calculation done by @5 at time 0.200000 DESCRIPTION: analysis data from calculation done by @5 at time 5.000000
REMARK TYPE=UNKNOWN
REMARK WEIGHT=1.0000 REMARK WEIGHT=1.0000
REMARK TYPE=OPTIMAL ATOM 1 X RES 0 -0.728 0.172 0.094 1.00 1.00
ATOM 1 X RES 0 -4.797 -10.892 -17.524 0.05 0.05 ATOM 2 X RES 1 10.307 0.085 8.601 1.00 1.00
ATOM 2 X RES 1 6.238 -10.978 -9.016 0.05 0.05 ATOM 3 X RES 2 8.579 8.613 0.861 1.00 1.00
ATOM 3 X RES 2 4.510 -2.450 -16.757 0.05 0.05 ATOM 4 X RES 3 -0.117 8.867 7.523 1.00 1.00
ATOM 4 X RES 3 -4.186 -2.197 -10.094 0.05 0.05 ATOM 5 X RES 4 -0.086 1.559 15.568 1.00 1.00
ATOM 5 X RES 4 -4.154 -9.504 -2.049 0.05 0.05 ATOM 6 X RES 5 8.626 1.178 24.895 1.00 1.00
ATOM 6 X RES 5 4.557 -9.886 7.278 0.05 0.05 ATOM 7 X RES 6 8.947 8.175 16.391 1.00 1.00
ATOM 7 X RES 6 4.879 -2.888 -1.227 0.05 0.05 ATOM 8 X RES 7 -0.826 7.508 25.139 1.00 1.00
ATOM 8 X RES 7 -4.895 -3.556 7.522 0.05 0.05 ATOM 9 X RES 8 -2.324 0.053 33.927 1.00 1.00
ATOM 9 X RES 8 -6.393 -11.011 16.310 0.05 0.05 ATOM 10 X RES 9 6.566 -0.118 42.281 1.00 1.00
ATOM 10 X RES 9 2.498 -11.182 24.664 0.05 0.05 ATOM 11 X RES 10 9.356 9.203 33.310 1.00 1.00
ATOM 11 X RES 10 5.288 -1.860 15.693 0.05 0.05 ATOM 12 X RES 11 0.208 9.501 42.205 1.00 1.00
ATOM 12 X RES 11 -3.861 -1.562 24.588 0.05 0.05 ATOM 13 X RES 12 1.056 16.641 -0.477 1.00 1.00
ATOM 13 X RES 12 -3.013 5.578 -18.094 0.05 0.05 ATOM 14 X RES 13 7.283 17.274 7.849 1.00 1.00
ATOM 14 X RES 13 3.214 6.210 -9.768 0.05 0.05 ATOM 15 X RES 14 9.103 24.770 -1.044 1.00 1.00
ATOM 15 X RES 14 5.034 13.706 -18.661 0.05 0.05 ATOM 16 X RES 15 0.688 25.236 7.617 1.00 1.00
ATOM 16 X RES 15 -3.380 14.173 -10.000 0.05 0.05 ATOM 17 X RES 16 -1.428 16.741 18.280 1.00 1.00
ATOM 17 X RES 16 -5.496 5.677 0.663 0.05 0.05 ATOM 18 X RES 17 7.031 15.181 24.387 1.00 1.00
ATOM 18 X RES 17 2.962 4.118 6.770 0.05 0.05 ATOM 19 X RES 18 8.450 24.859 18.490 1.00 1.00
ATOM 19 X RES 18 4.381 13.795 0.873 0.05 0.05 ATOM 20 X RES 19 0.682 25.773 26.448 1.00 1.00
ATOM 20 X RES 19 -3.386 14.709 8.831 0.05 0.05
END END
DESCRIPTION: analysis data from calculation done by @5 at time 0.200000 DESCRIPTION: analysis data from calculation done by @5 at time 5.000000
REMARK TYPE=UNKNOWN
REMARK WEIGHT=1.0000 REMARK WEIGHT=1.0000
REMARK TYPE=OPTIMAL ATOM 1 X RES 0 -0.874 0.351 0.130 1.00 1.00
ATOM 1 X RES 0 -4.972 -10.651 -17.468 0.05 0.05 ATOM 2 X RES 1 10.933 0.401 8.979 1.00 1.00
ATOM 2 X RES 1 6.834 -10.601 -8.619 0.05 0.05 ATOM 3 X RES 2 8.938 8.548 0.685 1.00 1.00
ATOM 3 X RES 2 4.839 -2.454 -16.913 0.05 0.05 ATOM 4 X RES 3 -0.586 8.592 7.357 1.00 1.00
ATOM 4 X RES 3 -4.685 -2.410 -10.241 0.05 0.05 ATOM 5 X RES 4 -0.086 2.284 15.670 1.00 1.00
ATOM 5 X RES 4 -4.184 -8.718 -1.928 0.05 0.05 ATOM 6 X RES 5 8.720 1.584 25.127 1.00 1.00
ATOM 6 X RES 5 4.622 -9.418 7.529 0.05 0.05 ATOM 7 X RES 6 9.208 8.030 16.125 1.00 1.00
ATOM 7 X RES 6 5.110 -2.972 -1.473 0.05 0.05 ATOM 8 X RES 7 -1.221 7.582 25.082 1.00 1.00
ATOM 8 X RES 7 -5.319 -3.420 7.484 0.05 0.05 ATOM 9 X RES 8 -3.001 -0.269 34.055 1.00 1.00
ATOM 9 X RES 8 -7.099 -11.271 16.457 0.05 0.05 ATOM 10 X RES 9 5.894 -0.422 42.134 1.00 1.00
ATOM 10 X RES 9 1.795 -11.424 24.536 0.05 0.05 ATOM 11 X RES 10 10.110 8.768 33.258 1.00 1.00
ATOM 11 X RES 10 6.011 -2.234 15.660 0.05 0.05 ATOM 12 X RES 11 0.852 9.331 42.351 1.00 1.00
ATOM 12 X RES 11 -3.246 -1.671 24.754 0.05 0.05 ATOM 13 X RES 12 1.565 16.847 -0.959 1.00 1.00
ATOM 13 X RES 12 -2.534 5.845 -18.557 0.05 0.05 ATOM 14 X RES 13 7.466 17.366 8.108 1.00 1.00
ATOM 14 X RES 13 3.368 6.364 -9.489 0.05 0.05 ATOM 15 X RES 14 9.273 24.641 -0.976 1.00 1.00
ATOM 15 X RES 14 5.174 13.639 -18.574 0.05 0.05 ATOM 16 X RES 15 0.732 25.134 7.562 1.00 1.00
ATOM 16 X RES 15 -3.367 14.132 -10.036 0.05 0.05 ATOM 17 X RES 16 -1.984 16.706 17.747 1.00 1.00
ATOM 17 X RES 16 -6.083 5.704 0.149 0.05 0.05 ATOM 18 X RES 17 7.489 14.803 24.434 1.00 1.00
ATOM 18 X RES 17 3.390 3.801 6.837 0.05 0.05 ATOM 19 X RES 18 8.315 24.535 18.345 1.00 1.00
ATOM 19 X RES 18 4.216 13.533 0.747 0.05 0.05 ATOM 20 X RES 19 0.228 25.227 26.742 1.00 1.00
ATOM 20 X RES 19 -3.871 14.225 9.145 0.05 0.05
END END
DESCRIPTION: analysis data from calculation done by @5 at time 0.200000 DESCRIPTION: analysis data from calculation done by @5 at time 5.000000
REMARK TYPE=UNKNOWN
REMARK WEIGHT=1.0000 REMARK WEIGHT=1.0000
REMARK TYPE=OPTIMAL ATOM 1 X RES 0 -0.914 0.528 0.408 1.00 1.00
ATOM 1 X RES 0 -5.103 -10.424 -17.164 0.05 0.05 ATOM 2 X RES 1 11.239 0.563 9.041 1.00 1.00
ATOM 2 X RES 1 7.050 -10.389 -8.531 0.05 0.05 ATOM 3 X RES 2 9.332 8.608 0.482 1.00 1.00
ATOM 3 X RES 2 5.143 -2.344 -17.090 0.05 0.05 ATOM 4 X RES 3 -0.918 8.759 7.023 1.00 1.00
ATOM 4 X RES 3 -5.107 -2.193 -10.548 0.05 0.05 ATOM 5 X RES 4 -0.138 2.562 15.913 1.00 1.00
ATOM 5 X RES 4 -4.327 -8.390 -1.659 0.05 0.05 ATOM 6 X RES 5 8.848 2.121 25.253 1.00 1.00
ATOM 6 X RES 5 4.658 -8.831 7.681 0.05 0.05 ATOM 7 X RES 6 9.337 8.252 15.736 1.00 1.00
ATOM 7 X RES 6 5.148 -2.700 -1.836 0.05 0.05 ATOM 8 X RES 7 -1.372 7.983 25.150 1.00 1.00
ATOM 8 X RES 7 -5.562 -2.969 7.578 0.05 0.05 ATOM 9 X RES 8 -3.304 -0.600 33.927 1.00 1.00
ATOM 9 X RES 8 -7.494 -11.552 16.355 0.05 0.05 ATOM 10 X RES 9 5.306 -0.610 41.956 1.00 1.00
ATOM 10 X RES 9 1.117 -11.563 24.384 0.05 0.05 ATOM 11 X RES 10 10.704 8.266 33.441 1.00 1.00
ATOM 11 X RES 10 6.514 -2.686 15.870 0.05 0.05 ATOM 12 X RES 11 1.399 8.949 42.393 1.00 1.00
ATOM 12 X RES 11 -2.790 -2.003 24.821 0.05 0.05 ATOM 13 X RES 12 2.252 16.950 -0.918 1.00 1.00
ATOM 13 X RES 12 -1.938 5.998 -18.490 0.05 0.05 ATOM 14 X RES 13 7.938 17.231 8.546 1.00 1.00
ATOM 14 X RES 13 3.749 6.279 -9.026 0.05 0.05 ATOM 15 X RES 14 9.405 24.564 -0.640 1.00 1.00
ATOM 15 X RES 14 5.216 13.612 -18.212 0.05 0.05 ATOM 16 X RES 15 0.939 25.094 7.667 1.00 1.00
ATOM 16 X RES 15 -3.250 14.142 -9.905 0.05 0.05 ATOM 17 X RES 16 -2.267 16.333 16.907 1.00 1.00
ATOM 17 X RES 16 -6.457 5.381 -0.665 0.05 0.05 ATOM 18 X RES 17 8.048 14.469 24.379 1.00 1.00
ATOM 18 X RES 17 3.858 3.517 6.807 0.05 0.05 ATOM 19 X RES 18 8.189 24.322 18.133 1.00 1.00
ATOM 19 X RES 18 3.999 13.370 0.561 0.05 0.05 ATOM 20 X RES 19 -0.233 24.697 26.640 1.00 1.00
ATOM 20 X RES 19 -4.422 13.745 9.068 0.05 0.05
END END
regtest/analysis/rt-read-dissims2/plumed.dat
+ 2
− 2
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c1: COLLECT_FRAMES ATOMS=1-20 STRIDE=1 USE_ALL_DATA c1: COLLECT_FRAMES ATOMS=1-20 STRIDE=1
r1: READ_DISSIMILARITY_MATRIX FRAMES=c1 FILE=mymatrix.dat r1: READ_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=c1 FILE=mymatrix.dat
PRINT_DISSIMILARITY_MATRIX USE_OUTPUT_DATA_FROM=r1 FILE=mymatrix_out.dat FMT=%8.4f 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 l1: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=r1 NLANDMARKS=5
......
regtest/analysis/rt-read-dissims2/traj.xyz 0 → 100644
+ 660
− 0
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regtest/analysis/rt-reselect-land/config
+ 2
− 2
View file @ debe8341
type=driver type=driver
# this is to test a different name # this is to test a different name
arg="--plumed plumed.dat --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f" arg="--plumed plumed.dat --ixyz traj.xyz"
extra_files="../../trajectories/trajectory.xyz" extra_files="../rt-read-dissims2/traj.xyz"
regtest/analysis/rt-reselect-land/plumed.dat
+ 5
− 2
View file @ debe8341
dist: DISTANCE ATOMS=1,2 dist: DISTANCE ATOMS=1,2
ss1: EUCLIDEAN_DISSIMILARITIES ATOMS=1-5 METRIC=OPTIMAL STRIDE=1 USE_ALL_DATA ff1: COLLECT_FRAMES ATOMS=1-5 STRIDE=1
ss2: EUCLIDEAN_DISSIMILARITIES ARG=dist STRIDE=1 USE_ALL_DATA ss1: EUCLIDEAN_DISSIMILARITIES USE_OUTPUT_DATA_FROM=ff1
ff2: COLLECT_FRAMES ARG=dist STRIDE=1
ss2: EUCLIDEAN_DISSIMILARITIES USE_OUTPUT_DATA_FROM=ff2
l1: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=ss1 NLANDMARKS=2 l1: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=ss1 NLANDMARKS=2
l2: RESELECT_LANDMARKS USE_OUTPUT_DATA_FROM=ss2 LANDMARKS=l1 l2: RESELECT_LANDMARKS USE_OUTPUT_DATA_FROM=ss2 LANDMARKS=l1
......
regtest/analysis/rt-store-print/output-all.pdb.reference
+ 0
− 1
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#! FIELDS d1 weight #! FIELDS d1 weight
0.000000 1.000000 0.000000 1.000000
0.000000 1.000000
1.000000 1.000000 1.000000 1.000000
2.000000 1.000000 2.000000 1.000000
3.000000 1.000000 3.000000 1.000000
......
regtest/analysis/rt-store-print/output-reuse.pdb.reference
+ 0
− 1
View file @ debe8341
#! FIELDS d1 weight #! FIELDS d1 weight
0.000000 1.000000 0.000000 1.000000
0.000000 1.000000
1.000000 1.000000 1.000000 1.000000
2.000000 1.000000 2.000000 1.000000
3.000000 1.000000 3.000000 1.000000
......
regtest/analysis/rt-store-print/output-stride.pdb.reference
+ 4
− 4
View file @ debe8341
#! FIELDS d1 weight #! FIELDS d1 weight
0.000000 1.000000 0.000000 1.000000
1.000000 1.000000 2.000000 1.000000
3.000000 1.000000 4.000000 1.000000
5.000000 1.000000 6.000000 1.000000
7.000000 1.000000 8.000000 1.000000
regtest/analysis/rt-store-print/plumed.dat
+ 7
− 5
View file @ debe8341
d1: READ FILE=colv_in VALUES=data d1: READ FILE=colv_in VALUES=data
ss1: OUTPUT_ANALYSIS_DATA_TO_COLVAR STRIDE=1 RUN=6 ARG=d1 FILE=output-half.pdb ff1: COLLECT_FRAMES STRIDE=1 ARG=d1 CLEAR=6
ss2: OUTPUT_ANALYSIS_DATA_TO_COLVAR STRIDE=1 USE_ALL_DATA ARG=d1 FILE=output-all.pdb ss1: OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=ff1 FILE=output-half.pdb STRIDE=6
ss3: OUTPUT_ANALYSIS_DATA_TO_COLVAR REUSE_INPUT_DATA_FROM=ss2 FILE=output-reuse.pdb ff2: COLLECT_FRAMES STRIDE=1 ARG=d1
ss2: OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=ff2 FILE=output-all.pdb
ss3: OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=ff2 FILE=output-reuse.pdb
ll1: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=ss3 NLANDMARKS=5 NOVORONOI ll1: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=ss3 NLANDMARKS=5 NOVORONOI
OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=ll1 FILE=output-stride.pdb p1: OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=ll1 FILE=output-stride.pdb
ll2: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=ss1 NLANDMARKS=3 NOVORONOI ll2: LANDMARK_SELECT_STRIDE USE_OUTPUT_DATA_FROM=ss1 NLANDMARKS=3 NOVORONOI
OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=ll2 FILE=output-stride2.pdb p2: OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=ll2 FILE=output-stride2.pdb STRIDE=6
regtest/dimred/rt-mds/analysis.0.embed.reference
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− 612
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regtest/dimred/rt-mds/analysis.0.list_embed.reference
+ 1
− 1
View file @ debe8341
...@@ -19,7 +19,7 @@ ...@@ -19,7 +19,7 @@
-0.0769 -0.0312 1.0000 -0.0769 -0.0312 1.0000
-0.0893 -0.0259 1.0000 -0.0893 -0.0259 1.0000
-0.0697 -0.0246 1.0000 -0.0697 -0.0246 1.0000
-0.0302 -0.0196 1.0000 -0.0301 -0.0196 1.0000
0.0093 -0.0072 1.0000 0.0093 -0.0072 1.0000
0.0274 0.0009 1.0000 0.0274 0.0009 1.0000
0.0301 0.0016 1.0000 0.0301 0.0016 1.0000
......
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