diff --git a/CHANGES/v2.4.txt b/CHANGES/v2.4.txt
index d50e0c880403d719dff2455759b97f18dc342b07..413f6a5bcab1f1bee68090563091bbafb2c7125b 100644
--- a/CHANGES/v2.4.txt
+++ b/CHANGES/v2.4.txt
@@ -14,9 +14,9 @@ Changes from version 2.3 which are relevant for users:
- The meaning of BIASFACTOR=1 in \ref METAD has been modified and can now be used to indicate unbiased
simulations. Non-well-tempered metadynamics is BIASFACTOR=-1, which is the new default value.
Notice that this has an implication on the biasfactor written in the HILLS file when doing
+ non-well-tempered metadynamics.
- \ref HISTOGRAM : When using weights default is now to output histogram divided by number of frames from which data was taken. In addition the
UNORMALIZED flag has been replaced with the keyword NORMALIZATION, which can be set equal to true, false or ndata.
- non-well-tempered metadynamics.
- New modules:
- A new EDS module have been included, contributed by Glen Hocky and Andrew White.
This module implements the following methods:
@@ -27,6 +27,7 @@ Changes from version 2.3 which are relevant for users:
- New actions:
- \ref INENVELOPE
- Other changes:
+ - \ref COMMITTOR : new flag to use committor to keep track of the visited basins without stopping the simulation
- \ref PBMETAD : multiple walkers using files (thanks to Marco De La Pierre).
- \ref PBMETAD : adaptive gaussians
- \ref PBMETAD : default names for GRID and FILE (usefull with many collective variables)
diff --git a/regtest/analysis/rt-commit-1/COMMITED.reference b/regtest/analysis/rt-commit-1/COMMITED.reference
new file mode 100644
index 0000000000000000000000000000000000000000..80eceb1d16854c01c0e8d877a1b2f3c1d51625ca
--- /dev/null
+++ b/regtest/analysis/rt-commit-1/COMMITED.reference
@@ -0,0 +1,5 @@
+#! FIELDS time x y basin
+ 10.000000 0.884956 0.295891 3
+#! FIELDS
+#! SET COMMITED TO BASIN 3
+
diff --git a/regtest/analysis/rt1/Makefile b/regtest/analysis/rt-commit-1/Makefile
similarity index 100%
rename from regtest/analysis/rt1/Makefile
rename to regtest/analysis/rt-commit-1/Makefile
diff --git a/regtest/analysis/rt1/ala12_trajectory.xyz b/regtest/analysis/rt-commit-1/ala12_trajectory.xyz
similarity index 100%
rename from regtest/analysis/rt1/ala12_trajectory.xyz
rename to regtest/analysis/rt-commit-1/ala12_trajectory.xyz
diff --git a/regtest/analysis/rt1/config b/regtest/analysis/rt-commit-1/config
similarity index 100%
rename from regtest/analysis/rt1/config
rename to regtest/analysis/rt-commit-1/config
diff --git a/regtest/analysis/rt1/plumed.dat b/regtest/analysis/rt-commit-1/plumed.dat
similarity index 100%
rename from regtest/analysis/rt1/plumed.dat
rename to regtest/analysis/rt-commit-1/plumed.dat
diff --git a/regtest/analysis/rt-commit-2/COMMITED.reference b/regtest/analysis/rt-commit-2/COMMITED.reference
new file mode 100644
index 0000000000000000000000000000000000000000..2f90b86a128f846323929401b1a884fd1063a50a
--- /dev/null
+++ b/regtest/analysis/rt-commit-2/COMMITED.reference
@@ -0,0 +1,8 @@
+#! FIELDS time x y basin
+ 0.000000 0.816365 0.323125 3
+ 2.000000 0.736343 0.306921 2
+ 3.000000 0.634412 0.367911 1
+ 8.000000 0.791258 0.312314 2
+ 9.000000 0.665771 0.321666 1
+ 10.000000 0.884956 0.295891 3
+ 11.000000 0.769426 0.312054 2
diff --git a/regtest/analysis/rt-commit-2/Makefile b/regtest/analysis/rt-commit-2/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/analysis/rt-commit-2/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/analysis/rt-commit-2/ala12_trajectory.xyz b/regtest/analysis/rt-commit-2/ala12_trajectory.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..ddf508adda823167b0ab6b2a0e0bdd87cdbf3fa4
--- /dev/null
+++ b/regtest/analysis/rt-commit-2/ala12_trajectory.xyz
@@ -0,0 +1,1608 @@
+132
+ 100. 100. 100.
+HH31 -0.9105 -0.2402 2.1804
+CH3 -0.893 -0.3352 2.2308
+HH32 -0.9504 -0.3501 2.3223
+HH33 -0.9067 -0.4173 2.1604
+C -0.745 -0.3303 2.2659
+O -0.6909 -0.2213 2.2834
+N -0.6812 -0.4475 2.2683
+H -0.7324 -0.5304 2.2418
+CA -0.5397 -0.4597 2.2969
+HA -0.4882 -0.386 2.2353
+CB -0.5075 -0.4366 2.4443
+HB1 -0.401 -0.4351 2.4674
+HB2 -0.5438 -0.5144 2.5114
+HB3 -0.5561 -0.3425 2.4701
+C -0.4909 -0.5948 2.2466
+O -0.4728 -0.6129 2.1264
+N -0.4848 -0.6965 2.3328
+H -0.5121 -0.679 2.4285
+CA -0.4722 -0.8399 2.3159
+HA -0.3768 -0.8522 2.2645
+CB -0.4609 -0.909 2.4515
+HB1 -0.376 -0.8709 2.5082
+HB2 -0.451 -1.0142 2.4246
+HB3 -0.5489 -0.9125 2.5158
+C -0.5753 -0.906 2.2256
+O -0.5359 -0.9754 2.1321
+N -0.7036 -0.8865 2.2568
+H -0.704 -0.8063 2.3182
+CA -0.8201 -0.9234 2.1789
+HA -0.7869 -0.9845 2.0949
+CB -0.9165 -0.9957 2.2726
+HB1 -0.8633 -1.0787 2.319
+HB2 -1.0099 -1.0329 2.2305
+HB3 -0.94 -0.9257 2.3527
+C -0.8724 -0.7907 2.1258
+O -0.8269 -0.6846 2.1676
+N -0.9566 -0.7899 2.0221
+H -0.963 -0.8819 1.981
+CA -0.9923 -0.6793 1.9356
+HA -1.0138 -0.5948 2.0009
+CB -0.8791 -0.6404 1.8409
+HB1 -0.8531 -0.7143 1.7651
+HB2 -0.7859 -0.629 1.8963
+HB3 -0.8983 -0.5483 1.7859
+C -1.1178 -0.7047 1.8532
+O -1.1516 -0.8217 1.8366
+N -1.1927 -0.6054 1.8049
+H -1.1603 -0.5097 1.8052
+CA -1.324 -0.6259 1.7469
+HA -1.3121 -0.716 1.6866
+CB -1.4367 -0.6396 1.8489
+HB1 -1.5329 -0.6504 1.799
+HB2 -1.4356 -0.5552 1.9178
+HB3 -1.4135 -0.7227 1.9155
+C -1.3632 -0.5087 1.6582
+O -1.3364 -0.3936 1.6918
+N -1.4207 -0.5433 1.5428
+H -1.4289 -0.644 1.5399
+CA -1.4898 -0.458 1.4482
+HA -1.5364 -0.3792 1.5074
+CB -1.3891 -0.38 1.3642
+HB1 -1.4478 -0.3098 1.3049
+HB2 -1.3232 -0.4434 1.3048
+HB3 -1.3289 -0.3155 1.4282
+C -1.5946 -0.517 1.3549
+O -1.7154 -0.5054 1.3744
+N -1.5477 -0.6023 1.2635
+H -1.4472 -0.6108 1.2571
+CA -1.6137 -0.7083 1.1902
+HA -1.7209 -0.703 1.2095
+CB -1.5913 -0.6901 1.0403
+HB1 -1.6476 -0.6072 0.9975
+HB2 -1.6105 -0.7811 0.9835
+HB3 -1.4837 -0.6728 1.042
+C -1.5549 -0.8405 1.2374
+O -1.4368 -0.8711 1.2226
+N -1.6457 -0.9114 1.3049
+H -1.7362 -0.8674 1.3143
+CA -1.6134 -1.0157 1.4001
+HA -1.7002 -1.0541 1.4537
+CB -1.5583 -1.1305 1.316
+HB1 -1.4572 -1.0975 1.2918
+HB2 -1.6217 -1.1496 1.2294
+HB3 -1.5599 -1.2271 1.3664
+C -1.5269 -0.9591 1.5119
+O -1.5214 -0.8375 1.5293
+N -1.4681 -1.0478 1.5924
+H -1.4907 -1.1462 1.5897
+CA -1.3672 -1.0148 1.691
+HA -1.3288 -0.9136 1.678
+CB -1.4348 -1.0169 1.8278
+HB1 -1.4897 -0.9229 1.8335
+HB2 -1.3581 -1.0251 1.9048
+HB3 -1.4889 -1.1094 1.8478
+C -1.2514 -1.1131 1.681
+O -1.267 -1.2212 1.6247
+N -1.1304 -1.0734 1.7209
+H -1.13 -0.9774 1.7523
+CA -1.0028 -1.1384 1.6987
+HA -1.0121 -1.2468 1.693
+CB -0.9496 -1.1025 1.5603
+HB1 -0.8583 -1.1593 1.5421
+HB2 -0.938 -0.9942 1.5574
+HB3 -1.0131 -1.1309 1.4763
+C -0.9012 -1.1121 1.8089
+O -0.9298 -1.0314 1.8971
+N -0.7836 -1.175 1.8022
+H -0.7676 -1.243 1.7292
+CA -0.6626 -1.1294 1.8676
+HA -0.6953 -1.0965 1.9663
+CB -0.5678 -1.2473 1.8875
+HB1 -0.5215 -1.271 1.7917
+HB2 -0.6285 -1.3303 1.9237
+HB3 -0.4881 -1.2167 1.9553
+C -0.6012 -1.0138 1.7899
+O -0.6378 -0.9893 1.6752
+N -0.5091 -0.9417 1.8543
+H -0.5077 -0.9637 1.9529
+CA -0.4233 -0.8407 1.7956
+HA -0.398 -0.8732 1.6947
+CB -0.4967 -0.7073 1.7857
+HB1 -0.4295 -0.6295 1.7497
+HB2 -0.5447 -0.6756 1.8783
+HB3 -0.5784 -0.7235 1.7154
+C -0.2955 -0.8248 1.8767
+O -0.1984 -0.8964 1.8535
+N -0.2923 -0.7389 1.9788
+H -0.3729 -0.6821 2.0007
+CH3 -0.169 -0.7089 2.0487
+HH31 -0.1873 -0.6629 2.1459
+HH32 -0.1152 -0.6284 1.9986
+HH33 -0.1135 -0.802 2.0602
+132
+ 100. 100. 100.
+HH31 -0.0219 -1.191 1.5105
+CH3 -0.0864 -1.2406 1.5831
+HH32 -0.0847 -1.3469 1.5589
+HH33 -0.0406 -1.21 1.6772
+C -0.2344 -1.2065 1.5741
+O -0.2955 -1.2489 1.4762
+N -0.2853 -1.1282 1.6694
+H -0.2187 -1.0759 1.7245
+CA -0.4235 -1.0892 1.6896
+HA -0.4673 -1.0542 1.5962
+CB -0.5079 -1.2066 1.7384
+HB1 -0.4738 -1.2388 1.8369
+HB2 -0.4883 -1.2957 1.6788
+HB3 -0.6136 -1.1803 1.7378
+C -0.433 -0.9747 1.7893
+O -0.3304 -0.9303 1.8405
+N -0.5529 -0.9232 1.8176
+H -0.6411 -0.9565 1.7815
+CA -0.5793 -0.8156 1.9109
+HA -0.5312 -0.8252 2.0082
+CB -0.5207 -0.6916 1.8438
+HB1 -0.5529 -0.6865 1.7398
+HB2 -0.4118 -0.6902 1.8479
+HB3 -0.5481 -0.6027 1.9007
+C -0.7286 -0.8068 1.9388
+O -0.7905 -0.909 1.9103
+N -0.7802 -0.7033 2.0056
+H -0.7241 -0.6197 2.014
+CA -0.9235 -0.6867 2.0193
+HA -0.9689 -0.7394 1.9354
+CB -0.9845 -0.7387 2.1491
+HB1 -0.9858 -0.8473 2.1587
+HB2 -1.0895 -0.7125 2.1618
+HB3 -0.9282 -0.6993 2.2338
+C -0.96 -0.539 2.0148
+O -0.8776 -0.4495 2.0322
+N -1.0834 -0.5032 1.9784
+H -1.1516 -0.5766 1.9655
+CA -1.1361 -0.3683 1.9729
+HA -1.0903 -0.3028 2.0469
+CB -1.0931 -0.3114 1.838
+HB1 -0.9846 -0.3015 1.8342
+HB2 -1.1172 -0.2057 1.8269
+HB3 -1.1314 -0.3669 1.7523
+C -1.2865 -0.3555 1.992
+O -1.3626 -0.3572 1.8954
+N -1.3298 -0.3484 2.1181
+H -1.2545 -0.3521 2.1853
+CA -1.4663 -0.3482 2.1668
+HA -1.466 -0.3689 2.2738
+CB -1.5284 -0.2094 2.1544
+HB1 -1.5105 -0.171 2.0539
+HB2 -1.487 -0.1423 2.2296
+HB3 -1.6336 -0.2122 2.1828
+C -1.5362 -0.4668 2.102
+O -1.5108 -0.585 2.1244
+N -1.628 -0.4369 2.0098
+H -1.6216 -0.3431 1.9729
+CA -1.7198 -0.5246 1.9399
+HA -1.7865 -0.5741 2.0105
+CB -1.8031 -0.4365 1.8472
+HB1 -1.738 -0.3886 1.7741
+HB2 -1.8407 -0.3588 1.9137
+HB3 -1.8712 -0.5025 1.7934
+C -1.6484 -0.6223 1.8476
+O -1.6973 -0.7339 1.8316
+N -1.5334 -0.5824 1.7928
+H -1.5008 -0.4927 1.8256
+CA -1.43 -0.6787 1.7604
+HA -1.4709 -0.7646 1.7071
+CB -1.3322 -0.6076 1.6673
+HB1 -1.2867 -0.6819 1.6018
+HB2 -1.2574 -0.5477 1.7194
+HB3 -1.3897 -0.5357 1.6089
+C -1.3783 -0.744 1.8878
+O -1.2754 -0.7043 1.9419
+N -1.4516 -0.8392 1.946
+H -1.5375 -0.8589 1.8967
+CA -1.4193 -0.9027 2.0722
+HA -1.4203 -0.8331 2.1561
+CB -1.5313 -0.9937 2.1218
+HB1 -1.5108 -1.0104 2.2275
+HB2 -1.531 -1.0911 2.073
+HB3 -1.6301 -0.955 2.0969
+C -1.283 -0.9703 2.0719
+O -1.2277 -0.9848 2.1807
+N -1.2428 -1.0209 1.9551
+H -1.3033 -1.0053 1.8758
+CA -1.1153 -1.079 1.918
+HA -1.031 -1.0405 1.9754
+CB -1.1265 -1.2294 1.9413
+HB1 -1.2104 -1.2731 1.8872
+HB2 -1.1258 -1.2557 2.0471
+HB3 -1.0427 -1.2859 1.9005
+C -1.0996 -1.0657 1.7672
+O -1.203 -1.0841 1.7033
+N -0.9801 -1.044 1.7119
+H -0.8965 -1.014 1.7599
+CA -0.9585 -1.0268 1.5696
+HA -1.0294 -1.0911 1.5176
+CB -0.9854 -0.8843 1.5221
+HB1 -0.9327 -0.8123 1.5847
+HB2 -1.0876 -0.8467 1.5268
+HB3 -0.9545 -0.8782 1.4178
+C -0.8182 -1.0788 1.5417
+O -0.7196 -1.01 1.5668
+N -0.8095 -1.1918 1.4711
+H -0.8987 -1.2324 1.4469
+CA -0.6941 -1.2497 1.4053
+HA -0.6155 -1.2477 1.4807
+CB -0.7292 -1.3942 1.3713
+HB1 -0.756 -1.4447 1.4641
+HB2 -0.6355 -1.4467 1.3525
+HB3 -0.8097 -1.4054 1.2986
+C -0.6431 -1.158 1.295
+O -0.717 -1.0939 1.2205
+N -0.5104 -1.1443 1.2904
+H -0.4543 -1.1902 1.3608
+CA -0.445 -1.0527 1.1991
+HA -0.5102 -1.0237 1.1167
+CB -0.3881 -0.9292 1.2683
+HB1 -0.2911 -0.9489 1.3138
+HB2 -0.4622 -0.8818 1.3327
+HB3 -0.3719 -0.8605 1.1852
+C -0.3321 -1.1209 1.1231
+O -0.3217 -1.1107 1.0011
+N -0.2494 -1.1958 1.1963
+H -0.2773 -1.2133 1.2918
+CH3 -0.1332 -1.261 1.1392
+HH31 -0.1207 -1.2177 1.0399
+HH32 -0.1485 -1.3687 1.1463
+HH33 -0.0426 -1.2334 1.193
+132
+ 100. 100. 100.
+HH31 -1.6971 -0.7275 1.7143
+CH3 -1.7139 -0.8178 1.773
+HH32 -1.8053 -0.7888 1.8246
+HH33 -1.7367 -0.9079 1.716
+C -1.589 -0.8338 1.8585
+O -1.5456 -0.7458 1.9326
+N -1.5306 -0.9516 1.8355
+H -1.5613 -1.0011 1.753
+CA -1.4323 -1.0036 1.9285
+HA -1.4523 -0.9535 2.0232
+CB -1.4528 -1.1536 1.9475
+HB1 -1.4072 -1.1914 2.0389
+HB2 -1.4099 -1.2008 1.8591
+HB3 -1.5546 -1.1883 1.9654
+C -1.2943 -0.9511 1.8914
+O -1.2802 -0.8546 1.8167
+N -1.1921 -1.0212 1.9408
+H -1.2008 -1.1194 1.9629
+CA -1.0574 -0.9712 1.9595
+HA -1.0534 -0.8904 2.0326
+CB -0.9822 -1.0882 2.0223
+HB1 -0.974 -1.1813 1.9661
+HB2 -1.0313 -1.118 2.1149
+HB3 -0.8794 -1.0557 2.0384
+C -0.9952 -0.9177 1.8312
+O -0.9829 -0.9897 1.7324
+N -0.9499 -0.7931 1.8473
+H -0.9674 -0.7459 1.9349
+CA -0.8857 -0.7188 1.7408
+HA -0.8523 -0.7853 1.6611
+CB -0.9939 -0.6324 1.6765
+HB1 -1.0113 -0.5442 1.7382
+HB2 -1.0787 -0.6965 1.6526
+HB3 -0.9628 -0.587 1.5824
+C -0.7593 -0.6468 1.7854
+O -0.766 -0.5429 1.8507
+N -0.6453 -0.7113 1.7596
+H -0.6646 -0.7944 1.7056
+CA -0.5119 -0.6927 1.8131
+HA -0.467 -0.7915 1.8035
+CB -0.4362 -0.5878 1.732
+HB1 -0.4685 -0.4842 1.7425
+HB2 -0.4359 -0.6227 1.6288
+HB3 -0.3324 -0.5792 1.764
+C -0.5027 -0.6592 1.9613
+O -0.4531 -0.7414 2.038
+N -0.5453 -0.5399 2.0034
+H -0.5855 -0.4822 1.9309
+CA -0.5281 -0.4855 2.1366
+HA -0.5115 -0.5686 2.2052
+CB -0.4163 -0.3818 2.1419
+HB1 -0.3279 -0.4238 2.094
+HB2 -0.4036 -0.3417 2.2424
+HB3 -0.448 -0.2974 2.0807
+C -0.6608 -0.426 2.1816
+O -0.6714 -0.3774 2.294
+N -0.7685 -0.431 2.1028
+H -0.754 -0.4842 2.0182
+CA -0.9045 -0.4025 2.1438
+HA -0.9042 -0.4044 2.2528
+CB -0.9437 -0.2635 2.0944
+HB1 -0.8696 -0.1891 2.1236
+HB2 -1.0388 -0.2469 2.145
+HB3 -0.9441 -0.2668 1.9854
+C -0.9958 -0.5126 2.0917
+O -0.9507 -0.6247 2.0694
+N -1.1251 -0.4901 2.0672
+H -1.1656 -0.3977 2.0709
+CA -1.2236 -0.5864 2.0224
+HA -1.1619 -0.6659 1.9804
+CB -1.2928 -0.6434 2.146
+HB1 -1.3652 -0.7189 2.1153
+HB2 -1.3485 -0.5717 2.2062
+HB3 -1.2123 -0.688 2.2044
+C -1.3059 -0.5203 1.9128
+O -1.3462 -0.4054 1.9289
+N -1.3096 -0.5785 1.7927
+H -1.3009 -0.6786 1.8032
+CA -1.3674 -0.5239 1.6715
+HA -1.4483 -0.4578 1.7027
+CB -1.2678 -0.4304 1.6035
+HB1 -1.3028 -0.3692 1.5204
+HB2 -1.186 -0.4936 1.5687
+HB3 -1.2284 -0.3595 1.6763
+C -1.4309 -0.6228 1.5748
+O -1.5325 -0.5903 1.5137
+N -1.3812 -0.7462 1.5646
+H -1.3082 -0.771 1.6299
+CA -1.4167 -0.8492 1.469
+HA -1.5173 -0.8236 1.4357
+CB -1.3122 -0.8398 1.3582
+HB1 -1.2105 -0.8307 1.3963
+HB2 -1.3282 -0.7448 1.3072
+HB3 -1.312 -0.928 1.2941
+C -1.4251 -0.9857 1.5359
+O -1.5352 -1.0286 1.5694
+N -1.3168 -1.0637 1.5358
+H -1.2321 -1.0164 1.5076
+CA -1.3208 -1.2027 1.5765
+HA -1.3976 -1.217 1.6525
+CB -1.3443 -1.2888 1.4527
+HB1 -1.2606 -1.2752 1.3842
+HB2 -1.4395 -1.2688 1.4035
+HB3 -1.3432 -1.3963 1.4705
+C -1.1884 -1.2384 1.6427
+O -1.182 -1.2473 1.7651
+N -1.0852 -1.2852 1.5721
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+HB2 -0.6007 -0.9561 1.4956
+HB3 -0.5859 -0.8874 1.3309
+C -0.8356 -1.1135 1.4243
+O -0.8497 -1.206 1.3446
+N -0.8677 -1.1272 1.5532
+H -0.848 -1.0541 1.62
+CA -0.9111 -1.2541 1.6079
+HA -0.8316 -1.3271 1.5925
+CB -0.9227 -1.2433 1.7597
+HB1 -0.9663 -1.3345 1.8004
+HB2 -1.0039 -1.1737 1.7809
+HB3 -0.8299 -1.2008 1.7978
+C -1.0426 -1.3057 1.5512
+O -1.0599 -1.4173 1.5026
+N -1.1411 -1.216 1.543
+H -1.1328 -1.1277 1.5914
+CA -1.2738 -1.2403 1.4902
+HA -1.3137 -1.3313 1.535
+CB -1.3597 -1.1237 1.5385
+HB1 -1.3433 -1.1114 1.6455
+HB2 -1.4618 -1.1565 1.5189
+HB3 -1.348 -1.0373 1.4731
+C -1.2747 -1.2495 1.3383
+O -1.3512 -1.3262 1.2802
+N -1.1922 -1.1707 1.269
+H -1.1237 -1.1077 1.3083
+CA -1.1513 -1.1982 1.1327
+HA -1.2372 -1.176 1.0693
+CB -1.0416 -1.1019 1.0881
+HB1 -1.034 -1.1113 0.9798
+HB2 -0.9443 -1.1358 1.1235
+HB3 -1.0724 -1.0009 1.1152
+C -1.0894 -1.3328 1.098
+O -1.1352 -1.3977 1.0042
+N -0.9896 -1.387 1.1682
+H -0.9408 -1.3202 1.226
+CA -0.9417 -1.5219 1.1456
+HA -0.9183 -1.533 1.0397
+CB -0.8119 -1.5322 1.2252
+HB1 -0.7397 -1.4552 1.1982
+HB2 -0.7645 -1.6289 1.2085
+HB3 -0.8257 -1.5162 1.3322
+C -1.0474 -1.6237 1.1859
+O -1.0773 -1.7205 1.1162
+N -1.0886 -1.6161 1.3126
+H -1.0569 -1.5344 1.3629
+CH3 -1.1572 -1.7212 1.385
+HH31 -1.195 -1.794 1.3133
+HH32 -1.2449 -1.6718 1.4269
+HH33 -1.087 -1.7662 1.4552
+132
+ 100. 100. 100.
+HH31 -0.2903 -0.4936 2.2511
+CH3 -0.3554 -0.4221 2.3013
+HH32 -0.3134 -0.3702 2.3875
+HH33 -0.3845 -0.3471 2.2278
+C -0.4693 -0.5062 2.3572
+O -0.4404 -0.6134 2.4099
+N -0.5902 -0.4497 2.3617
+H -0.606 -0.3656 2.3079
+CA -0.7023 -0.4967 2.4405
+HA -0.6978 -0.6055 2.4363
+CB -0.6758 -0.4641 2.5872
+HB1 -0.5739 -0.4911 2.6149
+HB2 -0.7353 -0.5343 2.6456
+HB3 -0.6909 -0.3588 2.611
+C -0.8361 -0.4435 2.3912
+O -0.8479 -0.4099 2.2736
+N -0.9318 -0.4365 2.484
+H -0.9173 -0.4698 2.5783
+CA -1.0652 -0.3821 2.4689
+HA -1.1217 -0.4317 2.5479
+CB -1.0601 -0.2317 2.494
+HB1 -1.1624 -0.1962 2.4817
+HB2 -0.9933 -0.1823 2.4235
+HB3 -1.0219 -0.2109 2.594
+C -1.1273 -0.4334 2.3397
+O -1.146 -0.5518 2.3125
+N -1.1584 -0.338 2.2517
+H -1.1465 -0.2436 2.2858
+CA -1.2114 -0.361 2.1188
+HA -1.2996 -0.4233 2.1335
+CB -1.2354 -0.2218 2.0611
+HB1 -1.2804 -0.2439 1.9642
+HB2 -1.1446 -0.1632 2.0471
+HB3 -1.2965 -0.1578 2.1247
+C -1.1097 -0.4227 2.0238
+O -1.145 -0.4982 1.9335
+N -0.983 -0.3817 2.0324
+H -0.9502 -0.3307 2.1133
+CA -0.8819 -0.4197 1.9358
+HA -0.9196 -0.3863 1.8391
+CB -0.7542 -0.337 1.9474
+HB1 -0.6826 -0.3634 1.8695
+HB2 -0.7092 -0.3472 2.0461
+HB3 -0.7687 -0.2325 1.92
+C -0.8642 -0.5708 1.9317
+O -0.8759 -0.627 1.8231
+N -0.8504 -0.6334 2.0489
+H -0.8457 -0.5752 2.1313
+CA -0.8501 -0.7758 2.0754
+HA -0.7596 -0.8264 2.0419
+CB -0.8502 -0.8017 2.2258
+HB1 -0.8422 -0.9104 2.2284
+HB2 -0.9411 -0.7669 2.2749
+HB3 -0.7644 -0.7542 2.2734
+C -0.9644 -0.8426 2.0003
+O -0.9443 -0.9298 1.9161
+N -1.088 -0.8017 2.0301
+H -1.0928 -0.7245 2.0951
+CA -1.2132 -0.8486 1.9741
+HA -1.2101 -0.9541 2.0013
+CB -1.3285 -0.7762 2.043
+HB1 -1.3551 -0.817 2.1405
+HB2 -1.4177 -0.7965 1.9837
+HB3 -1.3135 -0.6683 2.0477
+C -1.2179 -0.8401 1.8222
+O -1.2545 -0.938 1.7575
+N -1.1825 -0.7259 1.7628
+H -1.1632 -0.6471 1.823
+CA -1.1576 -0.7141 1.6206
+HA -1.252 -0.7467 1.5768
+CB -1.1186 -0.5684 1.5976
+HB1 -1.1223 -0.5491 1.4903
+HB2 -1.0201 -0.5462 1.6385
+HB3 -1.1878 -0.5004 1.6472
+C -1.0519 -0.8129 1.5735
+O -1.0699 -0.8821 1.4735
+N -0.9422 -0.8269 1.6483
+H -0.9334 -0.7637 1.7266
+CA -0.8342 -0.9176 1.615
+HA -0.797 -0.897 1.5146
+CB -0.7092 -0.9012 1.701
+HB1 -0.6274 -0.946 1.6446
+HB2 -0.7271 -0.9402 1.8012
+HB3 -0.688 -0.7949 1.7123
+C -0.8863 -1.0605 1.6093
+O -0.8634 -1.1312 1.5114
+N -0.9608 -1.1038 1.7113
+H -0.9734 -1.0496 1.7956
+CA -1.0241 -1.2339 1.7036
+HA -0.9468 -1.3089 1.6868
+CB -1.0865 -1.2775 1.8358
+HB1 -1.0134 -1.289 1.9159
+HB2 -1.1333 -1.3758 1.83
+HB3 -1.168 -1.2074 1.8536
+C -1.1252 -1.242 1.5902
+O -1.1313 -1.3381 1.5137
+N -1.2077 -1.1404 1.5641
+H -1.2028 -1.058 1.6224
+CA -1.324 -1.1571 1.4793
+HA -1.3825 -1.244 1.5092
+CB -1.4149 -1.0357 1.4962
+HB1 -1.4666 -1.0421 1.592
+HB2 -1.4958 -1.0505 1.4246
+HB3 -1.3665 -0.9383 1.4903
+C -1.2856 -1.171 1.3327
+O -1.3258 -1.2594 1.2572
+N -1.1988 -1.0808 1.2863
+H -1.1486 -1.0217 1.3509
+CA -1.1525 -1.0652 1.1498
+HA -1.2326 -1.086 1.079
+CB -1.1041 -0.9227 1.1245
+HB1 -1.0469 -0.9211 1.0317
+HB2 -1.0376 -0.8769 1.1977
+HB3 -1.1868 -0.8534 1.1089
+C -1.0402 -1.1612 1.1131
+O -1.0289 -1.1958 0.9957
+N -0.9564 -1.1942 1.2117
+H -0.98 -1.1503 1.2995
+CA -0.8413 -1.2797 1.191
+HA -0.8427 -1.3236 1.0913
+CB -0.7175 -1.1916 1.206
+HB1 -0.6353 -1.2626 1.2153
+HB2 -0.7221 -1.1471 1.3054
+HB3 -0.6859 -1.1207 1.1295
+C -0.8443 -1.4065 1.2751
+O -0.8599 -1.5134 1.2166
+N -0.8294 -1.4 1.4076
+H -0.8321 -1.3054 1.4429
+CH3 -0.8343 -1.5143 1.4966
+HH31 -0.9377 -1.534 1.5249
+HH32 -0.772 -1.496 1.5842
+HH33 -0.8059 -1.6078 1.4483
+132
+ 100. 100. 100.
+HH31 0.0719 -1.0155 1.8871
+CH3 0.0342 -0.9163 1.912
+HH32 0.0467 -0.8869 2.0162
+HH33 0.0759 -0.8309 1.8585
+C -0.1141 -0.9265 1.8792
+O -0.1527 -0.9711 1.7715
+N -0.207 -0.8868 1.9664
+H -0.1739 -0.8481 2.0537
+CA -0.3513 -0.8991 1.9619
+HA -0.3857 -0.9265 1.8622
+CB -0.4042 -0.9983 2.0651
+HB1 -0.5131 -0.9971 2.0713
+HB2 -0.3692 -0.9631 2.1621
+HB3 -0.3827 -1.1024 2.0408
+C -0.4146 -0.7633 1.989
+O -0.426 -0.7207 2.1038
+N -0.4567 -0.6923 1.8841
+H -0.4405 -0.7288 1.7914
+CA -0.5332 -0.5706 1.9021
+HA -0.4997 -0.5101 1.9864
+CB -0.5235 -0.4721 1.7859
+HB1 -0.4193 -0.4505 1.7626
+HB2 -0.5784 -0.3814 1.8111
+HB3 -0.5619 -0.5266 1.6997
+C -0.6786 -0.6104 1.9234
+O -0.7378 -0.6818 1.8428
+N -0.7386 -0.5626 2.0326
+H -0.6891 -0.5213 2.1103
+CA -0.8758 -0.5935 2.0677
+HA -0.869 -0.702 2.0753
+CB -0.9043 -0.5339 2.2052
+HB1 -0.8937 -0.4255 2.2001
+HB2 -0.8464 -0.5754 2.2878
+HB3 -1.0109 -0.5454 2.2246
+C -0.9806 -0.5565 1.9637
+O -0.9717 -0.4487 1.9055
+N -1.0786 -0.6443 1.9409
+H -1.0788 -0.7246 2.0021
+CA -1.1862 -0.6098 1.8502
+HA -1.1906 -0.5019 1.8354
+CB -1.1562 -0.6663 1.7116
+HB1 -1.1367 -0.7735 1.7121
+HB2 -1.0762 -0.6041 1.6713
+HB3 -1.2422 -0.65 1.6465
+C -1.3204 -0.6552 1.9057
+O -1.4251 -0.6002 1.8723
+N -1.3269 -0.7618 1.9858
+H -1.2354 -0.8025 1.9987
+CA -1.4369 -0.8189 2.0609
+HA -1.3936 -0.9179 2.075
+CB -1.4608 -0.7508 2.1953
+HB1 -1.5586 -0.7846 2.2295
+HB2 -1.4787 -0.6446 2.1785
+HB3 -1.38 -0.7852 2.26
+C -1.5681 -0.8331 1.985
+O -1.6073 -0.9436 1.9481
+N -1.6389 -0.722 1.9636
+H -1.5783 -0.6474 1.9949
+CA -1.7493 -0.7011 1.8721
+HA -1.8316 -0.7528 1.9214
+CB -1.7833 -0.5525 1.8657
+HB1 -1.6943 -0.4895 1.8649
+HB2 -1.8483 -0.5227 1.948
+HB3 -1.839 -0.5205 1.7776
+C -1.7285 -0.7617 1.734
+O -1.8055 -0.8434 1.684
+N -1.6168 -0.729 1.6686
+H -1.546 -0.681 1.7222
+CA -1.5961 -0.7596 1.5284
+HA -1.6882 -0.7901 1.4788
+CB -1.5475 -0.6349 1.455
+HB1 -1.6191 -0.5541 1.4704
+HB2 -1.5413 -0.6569 1.3485
+HB3 -1.4476 -0.6202 1.496
+C -1.5095 -0.8841 1.5152
+O -1.4058 -0.8883 1.4494
+N -1.5555 -0.9846 1.5901
+H -1.6492 -0.9732 1.6261
+CA -1.4801 -1.0903 1.6544
+HA -1.5514 -1.1318 1.7257
+CB -1.4528 -1.209 1.5625
+HB1 -1.418 -1.1685 1.4675
+HB2 -1.5439 -1.2671 1.5482
+HB3 -1.3694 -1.2653 1.6043
+C -1.362 -1.0423 1.7375
+O -1.3312 -0.9239 1.7488
+N -1.2996 -1.1343 1.8115
+H -1.3208 -1.2325 1.8012
+CA -1.2245 -1.1122 1.9334
+HA -1.2939 -1.0799 2.011
+CB -1.1615 -1.2439 1.978
+HB1 -1.0949 -1.282 1.9006
+HB2 -1.2379 -1.317 2.0044
+HB3 -1.1021 -1.2275 2.0679
+C -1.1102 -1.0129 1.9183
+O -1.1062 -0.9147 1.9921
+N -1.0125 -1.0363 1.8304
+H -1.0203 -1.1264 1.7855
+CA -0.8932 -0.9547 1.8205
+HA -0.9243 -0.8505 1.8286
+CB -0.7957 -0.9883 1.933
+HB1 -0.8397 -0.9534 2.0264
+HB2 -0.6989 -0.9381 1.9309
+HB3 -0.7885 -1.097 1.9337
+C -0.8255 -0.9767 1.6859
+O -0.8572 -1.0749 1.6193
+N -0.737 -0.8822 1.6536
+H -0.7309 -0.797 1.7076
+CA -0.6678 -0.8823 1.5262
+HA -0.6881 -0.9746 1.4719
+CB -0.7144 -0.77 1.434
+HB1 -0.8199 -0.7781 1.4078
+HB2 -0.6608 -0.7749 1.3392
+HB3 -0.7044 -0.6799 1.4945
+C -0.5176 -0.8814 1.5504
+O -0.467 -0.8196 1.6438
+N -0.4376 -0.9463 1.4654
+H -0.4807 -0.9842 1.3822
+CA -0.2927 -0.945 1.4648
+HA -0.2656 -0.9836 1.5631
+CB -0.2435 -1.0469 1.3624
+HB1 -0.2937 -1.0187 1.2698
+HB2 -0.2697 -1.1494 1.3885
+HB3 -0.135 -1.0426 1.3535
+C -0.2347 -0.8086 1.4304
+O -0.2774 -0.7438 1.3351
+N -0.1407 -0.7645 1.5143
+H -0.1028 -0.8276 1.5834
+CH3 -0.0782 -0.6355 1.4931
+HH31 0.0191 -0.6293 1.5417
+HH32 -0.1488 -0.5672 1.5404
+HH33 -0.0738 -0.6169 1.3857
diff --git a/regtest/analysis/rt-commit-2/config b/regtest/analysis/rt-commit-2/config
new file mode 100644
index 0000000000000000000000000000000000000000..fa70f44330ff9545bbea7735d153c0bda52786b7
--- /dev/null
+++ b/regtest/analysis/rt-commit-2/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz ala12_trajectory.xyz"
diff --git a/regtest/analysis/rt-commit-2/plumed.dat b/regtest/analysis/rt-commit-2/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..6e0f0ed02e950a1e7d36484e098c0ab650b61354
--- /dev/null
+++ b/regtest/analysis/rt-commit-2/plumed.dat
@@ -0,0 +1,18 @@
+x: DISTANCE ATOMS=1,20
+y: DISTANCE ATOMS=15,25
+
+COMMITTOR ...
+ARG=x,y
+BASIN_LL1=0.6,0.2
+BASIN_UL1=0.7,0.4
+BASIN_LL2=0.7,0.2
+BASIN_UL2=0.8,0.4
+BASIN_LL3=0.8,0.2
+BASIN_UL3=0.9,0.4
+FILE=COMMITED
+NOSTOP
+... COMMITTOR
+
+PRINT ARG=x,y FILE=COLVAR STRIDE=1
+
+ENDPLUMED
diff --git a/regtest/analysis/rt1/COMMITED.reference b/regtest/analysis/rt1/COMMITED.reference
deleted file mode 100644
index 27e4ce52056b610dbc9ed36914f0f93b67ed9f89..0000000000000000000000000000000000000000
--- a/regtest/analysis/rt1/COMMITED.reference
+++ /dev/null
@@ -1,5 +0,0 @@
-#! FIELDS time x y
- 10.000000 0.884956 0.295891
-#! FIELDS
-#! SET COMMITED TO BASIN 3
-
diff --git a/src/analysis/Committor.cpp b/src/analysis/Committor.cpp
index 870fb91f7766c86b57be68a9c4186e4f14c7a511..f7bf8baab3235a642647abf3e4637c8efd9b4f4a 100644
--- a/src/analysis/Committor.cpp
+++ b/src/analysis/Committor.cpp
@@ -64,6 +64,8 @@ private:
std::vector< std::vector<double> > lowerlimits;
std::vector< std::vector<double> > upperlimits;
unsigned nbasins;
+ unsigned basin;
+ bool doNotStop;
public:
static void registerKeywords( Keywords& keys );
explicit Committor(const ActionOptions&ao);
@@ -84,13 +86,16 @@ void Committor::registerKeywords( Keywords& keys ) {
keys.add("compulsory","STRIDE","1","the frequency with which the CVs are analysed");
keys.add("optional","FILE","the name of the file on which to output the reached basin");
keys.add("optional","FMT","the format that should be used to output real numbers");
+ keys.addFlag("NOSTOP",false,"if true do not stop the simulation when reaching a basin but just keep track of it");
}
Committor::Committor(const ActionOptions&ao):
Action(ao),
ActionPilot(ao),
ActionWithArguments(ao),
- fmt("%f")
+ fmt("%f"),
+ basin(0),
+ doNotStop(false)
{
ofile.link(*this);
parse("FILE",file);
@@ -105,10 +110,7 @@ Committor::Committor(const ActionOptions&ao):
fmt=" "+fmt;
log.printf(" with format %s\n",fmt.c_str());
- for(unsigned i=0; i<getNumberOfArguments(); ++i) ofile.setupPrintValue( getPntrToArgument(i) );
-
for(unsigned b=1;; ++b ) {
-
std::vector<double> tmpl, tmpu;
parseNumberedVector("BASIN_LL", b, tmpl );
parseNumberedVector("BASIN_UL", b, tmpu );
@@ -119,6 +121,9 @@ Committor::Committor(const ActionOptions&ao):
upperlimits.push_back(tmpu);
nbasins=b;
}
+
+ parseFlag("NOSTOP", doNotStop);
+
checkRead();
@@ -128,36 +133,57 @@ Committor::Committor(const ActionOptions&ao):
if(lowerlimits[b][i]>upperlimits[b][i]) error("COMMITTOR: UPPER bounds must always be greater than LOWER bounds");
log.printf(" %f - %f\n", lowerlimits[b][i], upperlimits[b][i]);
}
+ if(doNotStop) log.printf(" COMMITOR will keep track of the visited basins without stopping the simulations\n");
}
+
+ for(unsigned i=0; i<getNumberOfArguments(); ++i) ofile.setupPrintValue( getPntrToArgument(i) );
}
void Committor::calculate() {
std::vector<unsigned> inbasin;
inbasin.assign (nbasins,1);
+ // check if current configuration belongs to a basin
for(unsigned b=0; b<nbasins; ++b) {
for(unsigned i=0; i<getNumberOfArguments(); ++i) {
- if(getArgument(i)>lowerlimits[b][i]&&getArgument(i)<upperlimits[b][i]) inbasin[b]*=1; else inbasin[b]*=0;
+ if(getArgument(i)>lowerlimits[b][i]&&getArgument(i)<upperlimits[b][i]) {
+ inbasin[b]*=1;
+ } else {
+ inbasin[b]*=0;
+ }
}
}
+ // check in which basin we are if any and if this is the same or a new one
+ bool inonebasin = false;
for(unsigned b=0; b<nbasins; ++b) {
if(inbasin[b]==1) {
- ofile.fmtField(" %f");
- ofile.printField("time",getTime());
- for(unsigned i=0; i<getNumberOfArguments(); i++) {
- ofile.fmtField(fmt);
- ofile.printField( getPntrToArgument(i), getArgument(i) );
+ if(basin!=(b+1)) {
+ basin = b+1;
+ ofile.fmtField(" %f");
+ ofile.printField("time",getTime());
+ for(unsigned i=0; i<getNumberOfArguments(); i++) {
+ ofile.fmtField(fmt);
+ ofile.printField( getPntrToArgument(i), getArgument(i) );
+ }
+ ofile.printField("basin", static_cast<int> (b+1));
+ ofile.printField();
}
- ofile.printField();
- std::string num; Tools::convert( b+1, num );
- std::string str = "COMMITED TO BASIN " + num;
- ofile.addConstantField(str);
- ofile.printField();
- ofile.flush();
- plumed.stop();
+ inonebasin = true;
+ break;
}
}
+ if(!inonebasin) basin = 0;
+
+ // then check if the simulation should be stopped
+ if(inonebasin&&(!doNotStop)) {
+ std::string num; Tools::convert( basin, num );
+ std::string str = "COMMITED TO BASIN " + num;
+ ofile.addConstantField(str);
+ ofile.printField();
+ ofile.flush();
+ plumed.stop();
+ }
}
}
diff --git a/src/generic/Print.cpp b/src/generic/Print.cpp
index 69de0fd42d0e2d0f5189776679febd9db1ad10c9..2e7100162cf73532ed04b2595d7fc16a93455943 100644
--- a/src/generic/Print.cpp
+++ b/src/generic/Print.cpp
@@ -169,7 +169,6 @@ void Print::update() {
for(unsigned i=0; i<getNumberOfArguments(); i++) {
ofile.fmtField(fmt);
ofile.printField( getPntrToArgument(i), getArgument(i) );
- //ofile.printField(getPntrToArgument(i)->getName(),getArgument(i));
}
ofile.printField();
}
diff --git a/src/gridtools/ConvertToFES.cpp b/src/gridtools/ConvertToFES.cpp
index 4e77f435be378f1dce2f3bb413f46fae9fccd7e2..f9d3410ce725f3f0f911565e0433d5b7a96c4e39 100644
--- a/src/gridtools/ConvertToFES.cpp
+++ b/src/gridtools/ConvertToFES.cpp
@@ -32,7 +32,7 @@ This action allows you to take a free energy surface that was calculated using t
action and to convert it to a free energy surface. This transformation performed by doing:
\f[
-F(x) = -k_B T \ln H(x)\f$
+F(x) = -k_B T \ln H(x)
\f]
The free energy calculated on a grid is output by this action and can be printed using \ref DUMPGRID
diff --git a/src/mapping/PropertyMap.cpp b/src/mapping/PropertyMap.cpp
index 18630cfdd446a809e6215254106ed4bfc96d3ddf..b1e8445759588c417a6f759420d936f1e2c614bb 100644
--- a/src/mapping/PropertyMap.cpp
+++ b/src/mapping/PropertyMap.cpp
@@ -26,7 +26,7 @@
/*
Property maps but with a more flexible framework for the distance metric being used.
-This colvar calculates a property map using the formalism developed by Spiwork \cite Spiwok:2011ce.
+This colvar calculates a property map using the formalism developed by Spiwok \cite Spiwok:2011ce.
In essence if you have the value of some property, \f$X_i\f$, that it takes at a set of high-dimensional
positions then you calculate the value of the property at some arbitrary point in the high-dimensional space
using:
diff --git a/user-doc/tutorials/a-trieste-3.txt b/user-doc/tutorials/a-trieste-3.txt
index e846fe9aa865e3eaf5f9c9af2b43920375e3320d..c3939b6338d97b20e5616c06908d529c8a64db12 100644
--- a/user-doc/tutorials/a-trieste-3.txt
+++ b/user-doc/tutorials/a-trieste-3.txt
@@ -152,20 +152,23 @@ Notice the peak at 0.9 nm, this is the effect of using cut-off for the calculati
\section trieste-3-ex-2 Exercize 2: Apply a linear restraint on the same collective variable
Now we will try to apply a linear restraint on the relative distance and compare the resulting distribution.
The new sampling will reflect the effect of the bias.
+Be carefull about the statistics: in the simulation of exercise 1 you were postprocessing a trajectory of 125000 frames accumulating one frame every ten in an histogram and clearing
+the histogram after 10000 steps. As a result you had 12 blocks in the form of 11 analysis.* files and a final block named myhist.dat. In the following try to accumulate on the fly
+the same amount of statistics. Look into the .mdp file to see how often frames are written in a trajectory. If you write too many analysis.* files (i.e. 100 files plumed will fail
+with an error).
\plumedfile
# vim:ft=plumed
#compute the distance between the two oxygens
d: DISTANCE __FILL__
#accumulate block histograms
-hh: HISTOGRAM ARG=d KERNEL=DISCRETE __FILL__
+hh: HISTOGRAM ARG=d KERNEL=DISCRETE STRIDE=500 CLEAR=500000 GRID_MIN=0 GRID_MAX=4.0 GRID_BIN=200
#and dump them
DUMPGRID __FILL__
#apply a linear restraint
lr: RESTRAINT ARG=d KAPPA=0 AT=0 SLOPE=2.5
-
# Print the collective variable and the bias.
PRINT __FILL__
\endplumedfile
@@ -191,18 +194,31 @@ lr: RESTRAINT __FILL__
as: REWEIGHT_BIAS TEMP=298
HISTOGRAM ...
- __FILL__
LOGWEIGHTS=as
+ ARG=d
+ STRIDE=10
+ GRID_MIN=0 GRID_MAX=4.0 GRID_BIN=200
+ KERNEL=DISCRETE
+ CLEAR=10000
... HISTOGRAM
DUMPGRID __FILL__
PRINT ARG=*.* FILE=COLVAR STRIDE=1
\endplumedfile
+Be carefull again about the difference in the way statistics is accumulated on-the-fly or for post processising. This is not critical for the result but is important in order to have comparable histograms, that is histograms with comparable noise. Remember to give different names to the new histogram otherwise the one obtained before will be overwritten.
+
\verbatim
> plumed driver --mf_xtc traj_comp.xtc --plumed plumed.dat
\endverbatim
+\note To run block analysis of both sets of histograms you need to edit the python script because the file name is hardcoded.
+
+\verbatim
+> python3 do_block_histo.py > histo-biased.dat
+> python3 do_block_histo.py > histo-reweighted.dat
+\endverbatim
+
Now the resulting histogram should be comparable to the reference one.
\section trieste-3-ex-3 Exercize 3: Apply a quadratic restraint on the same collective variable
@@ -216,21 +232,28 @@ d: DISTANCE ATOMS=1,4
#apply the quadratic restraint centered at a distance of 0.5 nm
lr: RESTRAINT ARG=d KAPPA=10 AT=0.5
#accumulate the biased histogram
-hh: HISTOGRAM ARG=d STRIDE=1 GRID_MIN=0 GRID_MAX=4.0 GRID_BIN=200 KERNEL=DISCRETE CLEAR=100000
+hh: HISTOGRAM ARG=d STRIDE=500 GRID_MIN=0 GRID_MAX=4.0 GRID_BIN=200 KERNEL=DISCRETE CLEAR=500000
#dumpit
-DUMPGRID GRID=hh FILE=myhist.dat STRIDE=100000
+DUMPGRID GRID=hh FILE=myhist.dat STRIDE=500000
#calculate the weights from the constant bias
as: REWEIGHT_BIAS TEMP=298
#accumulate the unbiased histogram
-hhu: HISTOGRAM ARG=d STRIDE=1 GRID_MIN=0 GRID_MAX=4.0 GRID_BIN=200 KERNEL=DISCRETE CLEAR=100000 LOGWEIGHTS=as
+hhu: HISTOGRAM ARG=d STRIDE=500 GRID_MIN=0 GRID_MAX=4.0 GRID_BIN=200 KERNEL=DISCRETE CLEAR=500000 LOGWEIGHTS=as
#dumpit
-DUMPGRID GRID=hhu FILE=myhistu.dat STRIDE=100000
+DUMPGRID GRID=hhu FILE=myhistu.dat STRIDE=500000
#print distance and bias
PRINT ARG=d,lr.bias FILE=distance.dat STRIDE=50
\endplumedfile
The comparison of the two histograms with the former will show the effect of the weak quadratic bias on the simulation.
+\note To run block analysis of both sets of histograms you need to edit the python script because the file name is hardcoded.
+
+\verbatim
+> python3 do_block_histo.py > histo-biased.dat
+> python3 do_block_histo.py > histo-reweighted.dat
+\endverbatim
+
\section trieste-3-ex-4 Exercize 4: Apply an upper wall on the distance.
In the above cases we have always applied weak biases. Sometimes biases are usefull to prevent the system in reaching some region of the conformational space. In this case instead of using \ref RESTRAINT , we can make use of lower or upper restraints, e.g. \ref LOWER_WALLS and \ref UPPER_WALLS.
@@ -272,7 +295,7 @@ In this exercise we will make use of the free-energy estimate along the distance
#calculate the distance
d: DISTANCE ATOMS=1,4
#accumulate the histogram using a gaussian kernel with 0.05 nm width
-hh2: HISTOGRAM ARG=d STRIDE=1 GRID_MIN=0 GRID_MAX=4.0 GRID_BIN=400 BANDWIDTH=0.05
+hh2: HISTOGRAM ARG=d STRIDE=10 GRID_MIN=0 GRID_MAX=4.0 GRID_BIN=400 BANDWIDTH=0.05
#convert to a free energy
ff: CONVERT_TO_FES GRID=__FILL__ TEMP=__FILL__
#dump the free energy
@@ -365,8 +388,8 @@ As a first test lets run an MD and generate on-the-fly the free energy as a func
MOLINFO STRUCTURE=aladip.pdb
phi: TORSION ATOMS=@phi-2
psi: TORSION ATOMS=@psi-2
-hhphi: HISTOGRAM ARG=phi STRIDE=1 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=600 BANDWIDTH=0.05
-hhpsi: HISTOGRAM ARG=psi STRIDE=1 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=600 BANDWIDTH=0.05
+hhphi: HISTOGRAM ARG=phi STRIDE=10 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=600 BANDWIDTH=0.05
+hhpsi: HISTOGRAM ARG=psi STRIDE=10 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=600 BANDWIDTH=0.05
ffphi: CONVERT_TO_FES GRID=hhphi TEMP=298
ffpsi: CONVERT_TO_FES GRID=hhpsi TEMP=298
DUMPGRID GRID=ffphi FILE=ffphi.dat
@@ -465,8 +488,8 @@ PERIODIC=NO
b: BIASVALUE ARG=tripleg
as: REWEIGHT_BIAS TEMP=298
-hhphi: HISTOGRAM ARG=phi STRIDE=1 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=600 BANDWIDTH=0.05 LOGWEIGHTS=as
-hhpsi: HISTOGRAM ARG=psi STRIDE=1 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=600 BANDWIDTH=0.05 LOGWEIGHTS=as
+hhphi: HISTOGRAM ARG=phi STRIDE=10 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=600 BANDWIDTH=0.05 LOGWEIGHTS=as
+hhpsi: HISTOGRAM ARG=psi STRIDE=10 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=600 BANDWIDTH=0.05 LOGWEIGHTS=as
ffphi: CONVERT_TO_FES GRID=hhphi TEMP=298
ffpsi: CONVERT_TO_FES GRID=hhpsi TEMP=298
diff --git a/user-doc/tutorials/a-trieste-6.txt b/user-doc/tutorials/a-trieste-6.txt
index c3eea6fbd6ca547a0d4fd5ca1c23078c436ae301..68dea2c3347fdb706526ee296b94a3c5763a3208 100644
--- a/user-doc/tutorials/a-trieste-6.txt
+++ b/user-doc/tutorials/a-trieste-6.txt
@@ -34,6 +34,8 @@ In this tutorial we propose exercizes on the following biological systems:
- the cmyc peptide in presence of urea at low concentration (cmyc-urea)
- the protein G B1 domain
+The exercise are of increasing difficulties, inputs are partially provided for the first and second cases while for the last one the user is expected to be autonomous.
+
\section trieste-6-ex-1 Exercize 1: analysis of the BARD1 complex simulation
The BARD1 complex is a heterodimer composed by two domains of 112 and 117 residues each.
@@ -85,7 +87,7 @@ chainA: GROUP ATOMS=1,3,5,7,9,10,12,15,17,19,21,23,25,27,29,31,33,34,36,38,41,43
# backbone beads index for chain B
chainB: GROUP ATOMS=226,228,230,232,234,235,238,239,240,245,246,250,252,255,256,257,259,261,264,266,268,271,273,275,278,280,282,285,287,289,291,293,295,298,300,302,304,306,308,309,310,312,314,318,320,324,326,328,330,332,334,336,338,340,342,343,345,346,348,350,352,354,358,360,362,363,368,370,372,374,376,379,381,383,386,388,390,392,394,396,398,400,402,404,406,409,411,414,416,418,420,424,426,428,430,432,434
-coord: COORDINATION GROUPA=chainA GROUPB=chainB NOPBC D_0=1.0
+coord: COORDINATION GROUPA=chainA GROUPB=chainB NOPBC R_0=1.0
\endplumedfile
3) A CV describing the relative orientation of the two chains.
@@ -122,6 +124,7 @@ of a single molecule of urea.
using `VMD`.
The users are expected to:
+- characterize the conformational ensemble of cmyc by calculating free-energies as a function of different CVs.
- calculate the fraction of bound and unbound molecules of urea by defining suitable CVs to measure
the position of urea relative to cmyc.
- find the cmyc aminoacids that bind urea the most and the least.
@@ -138,12 +141,31 @@ the conformational landscape of cmyc:
2) the content of alpha (\ref ALPHARMSD) and beta (\ref ANTIBETARMSD) secondary structure
+The fraction of bound and unbound molecules of urea can be computed after evaluating the minimum distance
+among all the distances between heavy atoms of cmyc and urea, as follows:
+
+\plumedfile
+# cmyc heavy atoms
+cmyc: GROUP ATOMS=5,6,7,9,11,14,15,17,19,22,24,26,27,28,30,32,34,38,41,45,46,47,49,51,54,56,60,64,65,66,68,70,73,75,76,77,79,81,83,87,91,92,93,95,97,100,103,104,105,108,109,110,112,114,118,119,120,122,124,127,130,131,132,133,134,135,137,139,142,145,146,147,148,149,150,152,154,157,160,161,162,165,166,167,169,171,174,177,180,183,187,188
+
+# urea heavy atoms
+urea: GROUP ATOMS=192,193,194,197
+
+# minimum distance cmyc-urea
+mindist: DISTANCES GROUPA=cmyc GROUPB=urea MIN={BETA=50.}
+\endplumedfile
+
+For estimating the cmyc aminoacid that bind the most and the least urea, we leave the users the choice of the best
+strategy.
+
For the calculation of ensemble averages of experimental CVs, we suggest to use:
1) 3J scalar couplings (\ref JCOUPLING)
2) the FRET intensity between termini (\ref FRET)
+and we encourage the users to look at the examples provided in the manual for the exact syntax.
+
\section trieste-6-ex-3 Exercize 3: Protein G folding simulations
GB1 is a small protein domain with a simple beta-alpha-beta fold. It is a well studied protein that folds on the millisecond time scale.
Here we use a structure based potential and well-tempered metadynamics to study the free energy of folding and unfolding.
@@ -155,8 +177,8 @@ to bias the sampling.
The users are expected to:
- setup and perform a well-tempered metadynamics simulation
-- calculate the free energy difference between the folded and unfolded state of this protein
- evaluate convergence and error calculation of the metadynamics simulation
+- calculate the free energy difference between the folded and unfolded state of this protein
- evaluate the robustness of the former by reweighting the resulting free energy as function of different CVs
The users are free to choose his/her favorite CVs and they are encouraged to use the
@@ -166,11 +188,24 @@ the free-energy landscape of GB1:
- \ref RMSD with respect to the folded state
- \ref GYRATION
-- \ref ALPHABETA and \ref DIHCOR
+- \ref ALPHABETA
+- \ref DIHCOR
The users should select two of them for the \ref METAD simulation. Once you are satisfied by the convergence of your simulation, you can use one of the reweighting algorithms proposed
-to evaluate the free-energy difference between folded and unfolded state as a function of multiple collective variables.
+to evaluate the free-energy difference between folded and unfolded state as a function of multiple collective variables.
+
+\plumedfile
+#this allows you to use short-cut for dihedral angles
+MOLINFO STRUCTURE=GB1_native.pdb
+#add here the collective variables you want to bias
+
+#add here the METAD bias, remember that you need to set: one SIGMA per CV, one single HEIGHT, one BIASFACTOR and one PACE.
+#Using GRIDS can increase the performances, so set a as many GRID_MIN and GRID_MAX as the number of CVs with reasonable ranges
+#(i.e an RMSD will range between 0 and 3, while ALPHABETA and DIHCOR will range between 0 and N of dihedrals).
+
+#add here the printing
+\endplumedfile
\section trieste-6-conclusions Conclusions
@@ -186,5 +221,3 @@ In summary, in this tutorial you should have learned how to use PLUMED to:
link: @subpage trieste-6
description: This tutorial explains how to use PLUMED to run metadynamics simulations
-
-additional-files: trieste-6