[gmx-users] Plumed-2 WTMetadynamics PBC

tarak karmakar tarak20489 at gmail.com
Wed Jan 29 06:56:08 CET 2014 

Dear All,

I'm running a Well-Tempered Metadynamics simulation of gate opening and
ligand release of a protein in gromacs-4.5.5 patched with plumed-2.
Plumed.dat file is given below

COM ATOMS=1848-2074 LABEL=L1
COM ATOMS=3141-3329 LABEL=L2
DISTANCE ATOMS=L1,L2 LABEL=gate_width


COM ATOMS=2285-2361,2820-2841,3158-3209,3249-3300,3723,3724-3753
LABEL=pocket
COM ATOMS=3754-3769 LABEL=lig
DISTANCE ATOMS=pocket,lig LABEL=lig_dist

UPPER_WALLS ARG=gate_width,lig_dist AT=3.5,1.5 KAPPA=418.4,418.4 EXP=2,2
EPS=1,1 LABEL=uwall
PRINT ARG=uwall.bias


METAD ...
  ARG=gate_width,lig_dist
  LABEL=metadyn
  SIGMA=0.05,0.05 HEIGHT=0.4184 PACE=500 FILE=HILLS
  TEMP=300
  BIASFACTOR=15
... METAD
PRINT ARG=gate_width,lig_dist,metadyn.bias STRIDE=1000 FILE=COLVAR


I see sudden jump in the COLVAR file (CV1, 2nd column, unit = nm) even
though there is no drastic change in the loop positions (from the
visualization of the traj file in vmd).

Part of the COLVAR file

 2498.000119 1.299294 0.178184 37.415171
 2500.000119 1.119773 0.196934 31.933709
 2502.000119 1.571106 0.292974 46.436339
 2504.000119 1.117527 0.265851 25.695039
 2506.000119 1.485084 0.335118 27.552946
 2508.000119 1.497514 0.331746 29.994809
 2510.000119 1.661614 0.300489 35.275959
 2512.000119 1.170725 0.329365 8.534140
 2514.000119 1.415805 0.370130 9.169973
 2516.000120 1.323237 0.341279 7.594384
 2518.000120 1.412595 0.324066 20.260243
 2520.000120 1.500857 0.346253 26.124207
 2522.000120 1.538378 0.306981 41.099405
 2524.000120 1.193061 0.346137 6.111681
 2526.000120 1.567241 0.319277 38.178439
 2528.000120 1.491094 0.340200 27.710411
 2530.000120 1.406830 0.331275 17.694551
 2532.000120 1.633375 0.283206 47.226252
 2534.000120 1.508039 0.337235 30.208556
 2536.000120 2.003640 0.225248 0.861068
 2538.000121 2.153453 0.224874 0.358799
 2540.000121 2.399507 0.220631 0.000000
 2542.000121 2.471678 0.223390 0.292396
 2544.000121 2.480027 0.229807 0.751878
 2546.000121 2.543216 0.208791 0.335023
 2548.000121 2.390282 0.200305 1.628845
 2550.000121 2.621234 0.206944 0.158723
 2552.000121 2.641127 0.216846 0.459373
 2554.000121 2.583292 0.211736 1.315043
 2556.000121 2.803431 0.205930 0.096919
 2558.000121 2.726586 0.208674 1.117967
 2560.000122 2.766929 0.224461 1.362122
 2562.000122 2.793271 0.215269 1.843174
 2564.000122 2.871510 0.200427 0.564119
 2566.000122 2.768285 0.198214 2.961266
 2568.000122 2.796291 0.236823 3.360909
 2570.000122 2.854209 0.192992 1.755358
 2572.000122 2.771890 0.217612 4.651824
 2574.000122 2.819913 0.195541 3.995093
 2576.000122 2.786860 0.220732 5.939467
 2578.000122 2.805697 0.207105 6.082593
 2580.000123 2.780348 0.211569 7.194714
 2582.000123 2.846254 0.203671 4.897594
 2584.000123 2.843371 0.208545 5.857665
 2586.000123 2.777621 0.238376 7.545472
 2588.000123 2.832321 0.214143 7.640190
 2590.000123 2.783773 0.209728 9.514020
 2592.000123 2.829434 0.222657 8.683501
 2594.000123 2.740298 0.218146 7.609711
 2596.000123 2.758956 0.212447 9.877642
 2598.000123 2.675364 0.245748 2.874006
 2600.000123 2.829696 0.218012 9.902114
 2602.000124 2.788214 0.229802 12.191769
 2604.000124 2.801283 0.224541 12.757834
 2606.000124 2.785606 0.216950 13.526085
 2608.000124 2.837555 0.214740 10.632563
 2610.000124 2.833324 0.243154 10.484840
 2612.000124 2.815604 0.259484 10.363993
 2614.000124 2.843706 0.217691 11.560925
 2616.000124 2.842759 0.225842 12.154987
 2618.000124 2.849623 0.190150 10.280937
 2620.000124 2.851833 0.203370 11.712638
 2622.000125 2.845595 0.235609 12.854942
 2624.000125 2.873155 0.207009 9.668154
 2626.000125 2.838478 0.194582 13.996211
 2628.000125 2.811962 0.231318 17.294889
 2630.000125 2.857938 0.202568 13.118407
 2632.000125 2.824019 0.221172 18.117673
 2634.000125 2.847886 0.227647 15.850138
 2636.000125 2.823402 0.205390 18.297248
 2638.000125 2.879928 0.244770 9.792060
 2640.000125 2.856425 0.251009 13.435001
 2642.000125 2.864119 0.206776 14.744654
 2644.000126 2.890657 0.190726 9.083225
 2646.000126 2.831430 0.272032 12.582280
 2648.000126 2.815536 0.192829 18.674856
 2650.000126 2.873947 0.199392 13.957499
 2652.000126 2.854132 0.214714 18.808931
 2654.000126 2.783788 0.217576 19.736853
 2656.000126 2.805172 0.234948 21.384247
 2658.000126 2.858713 0.214108 18.880528
 2660.000126 2.855870 0.238113 18.362306
 2662.000126 2.631975 0.204377 2.229255
 2664.000127 2.815917 0.195793 21.797392
 2666.000127 2.654829 0.203538 3.305112
 2668.000127 2.704365 0.195172 7.081424
 2670.000127 2.714401 0.253165 7.703605
 2672.000127 2.695996 0.212933 7.710584
 2674.000127 2.621846 0.218194 3.740190
 2676.000127 2.773939 0.239132 19.648104
 2678.000127 2.749841 0.217941 17.422105
 2680.000127 2.712477 0.202162 10.789414
 2682.000127 2.781281 0.214734 23.292621
 2684.000127 2.733285 0.237803 14.592003
 2686.000128 2.492645 0.205147 2.502843
 2688.000128 2.787534 0.225355 24.699721
 2690.000128 2.788155 0.236444 23.943576
 2692.000128 2.799564 0.199257 24.566171
 2694.000128 2.807537 0.220608 26.785322
 2696.000128 2.782417 0.266553 17.283757
 2698.000128 2.707036 0.218319 12.581452
 2700.000128 2.745092 0.208694 20.069051
 2702.000128 2.734204 0.207862 18.341387
 2704.000128 2.672733 0.205131 8.671731
 2706.000129 2.650649 0.213824 7.132788
 2708.000129 2.774941 0.193322 23.489587
 2710.000129 2.780528 0.195848 24.935369
 2712.000129 2.759917 0.226301 24.816043
 2714.000129 2.754274 0.238990 22.822172
 2716.000129 2.725395 0.231348 18.827216
 2718.000129 2.691223 0.235295 12.511569
 2720.000129 2.734576 0.254364 17.904164
 2722.000129 2.697847 0.208173 14.554933
 2724.000129 2.774483 0.287628 13.187153
 2726.000129 2.734372 0.225715 22.847710
 2728.000130 2.720340 0.212098 20.308122
 2730.000130 2.750456 0.179717 19.969848
 2732.000130 2.757430 0.211971 27.719589
 2734.000130 2.742892 0.230371 25.655565
 2736.000130 2.745745 0.180560 20.613847
 2738.000130 2.719159 0.239950 20.541822
 2740.000130 2.737978 0.191541 22.877122
 2742.000130 2.746515 0.218523 28.167164
 2744.000130 2.754628 0.206346 28.897086
 2746.000130 2.762426 0.201232 29.364643
 2748.000131 2.778143 0.181394 25.404931
 2750.000131 2.748050 0.211124 29.377969
 2752.000131 2.751889 0.190510 26.552445
 2754.000131 2.687598 0.197520 15.354605
 2756.000131 2.758328 0.224315 31.898523
 2758.000131 2.696732 0.245039 17.153395
 2760.000131 2.682289 0.180799 12.521206
 2762.000131 2.694066 0.208285 18.747348
 2764.000131 2.522141 0.192278 2.783059
 2766.000131 2.011234 0.194901 1.272339
 2768.000131 1.689675 0.186805 44.190309
 2770.000132 2.047611 0.230570 1.662861
 2772.000132 1.965007 0.210066 2.712007
 2774.000132 1.865094 0.232848 5.102416
 2776.000132 1.870799 0.210012 5.666963


Then I checked the periodic boundary condition in the md.log file and it
seems it is activated. A small part of md.log file with PBC info.

PLUMED: Action DISTANCE
PLUMED:   with label gate_width
PLUMED:   between atoms 73539 73540
PLUMED:   using periodic boundary conditions

Please suggest me something to get rid of this problem.


regards,
Tarak
Molecular Simulations Lab.
JNCASR
Bangalore, India

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