[gmx-users] Plumed-2 WTMetadynamics PBC

Wed Jan 29 14:57:04 CET 2014

Dear Carlo,

I thought people who use plumed with gromacs would look into my post.
Thanks for looking at it. :)

Gareth Tribello has suggested me to use few options related to the pbc
implementation on COLVARS. I'm working on that.

cheers,
Tarak

On Wed, Jan 29, 2014 at 5:04 PM, Carlo Camilloni
<carlo.camilloni at gmail.com>wrote:

> 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
> >
>
> --
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