[gmx-users] Plumed-2 WTMetadynamics PBC

Wed Jan 29 12:34:18 CET 2014

Dear Tarak,

I think this message would me more appropriate for the PLUMED mailing list.
plumed-users at googlegroups.com

Best wishes,
Carlo

> Message: 3
> Date: Wed, 29 Jan 2014 11:17:46 +0530
> From: tarak karmakar <tarak20489 at gmail.com>
> To: plumed-users at googlegroups.com, 	Discussion list for GROMACS users
> 	<gmx-users at gromacs.org>
> Subject: [gmx-users] Plumed-2 WTMetadynamics PBC
> Message-ID:
> 	<CAGZMOovTxsHDHeoO-C8MKZbx6t7uoadQiPw-Pvh_87UyTgHPiQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> 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
> 