[gmx-users] Problem with simulation of Protein-DNA complex
rarora at ens-cachan.fr
rarora at ens-cachan.fr
Thu Feb 9 14:08:37 CET 2012
Hi Lina,
I am sorry, I think I forgot to mention that I did perform energy
minimisation using Steep-Descent for 5000 steps, before NVT.
I was so engrossed in other details that I forgot to mention it!
Quoting lina <lina.lastname at gmail.com>:
> On Thu, Feb 9, 2012 at 8:44 PM, <rarora at ens-cachan.fr> wrote:
>> Dear Gromacs users,
>>
>> I have been trying to simulate a Protein-DNA complex using gromacs, but each
>> time I have been facing problems. I would like to point out that both the
>> Protein and DNA have been modeled and after that docked in order to obtain a
>> complex. Following are the parameters I am using:
>>
>> Force-Field: amber99sb-ildn
>> water model: TIP3P
>>
>> 40 NA ions were added in order to neutralise the complex-solvent system.
>> Gromacs doesn't show any error up until I proceed to do nvt equilibriation.
>
> Before the NVT, you may do some energy minimization.
>
>
>> Following is nvt.mdp:
>>
>> title = PFV_DNA_NVT
>> define = -DPOSRES ; position restrain the protein
>> ; Run parameters
>> integrator = md ; leap-frog integrator
>> nsteps = 1000000 ; 2 * 50000 = 100 ps
>> dt = 0.001 ; 2 fs
>> ; Output control
>> nstxout = 100 ; save coordinates every 0.2 ps
>> nstvout = 100 ; save velocities every 0.2 ps
>> nstenergy = 100 ; save energies every 0.2 ps
>> nstlog = 100 ; update log file every 0.2 ps
>> ; Bond parameters
>> continuation = no ; first dynamics run
>> constraint_algorithm = lincs ; holonomic constraints
>> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
>> constrained
>> lincs_iter = 1 ; accuracy of LINCS
>> lincs_order = 4 ; also related to accuracyi
>> ; Neighborsearching
>> ns_type = grid ; search neighboring grid cels
>> nstlist = 5 ; 10 fs
>> rlist = 1.0 ; short-range neighborlist cutoff (in nm)
>> rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
>> rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
>> ; Electrostatics
>> coulombtype = PME ; Particle Mesh Ewald for long-range
>> electrostatics
>> pme_order = 4 ; cubic interpolation
>> fourierspacing = 0.16 ; grid spacing for FFT
>> ; Temperature coupling is on
>> tcoupl = V-rescale ; modified Berendsen thermostat
>> tc-grps = Protein Non-Protein
>> tau_t = 0.1 0.1 ; time constant, in ps
>> ref_t = 300 300 ; reference temperature, one for each group,
>> in K
>> ; Pressure coupling is off
>> pcoupl = no ; no pressure coupling in NVT
>> ; Periodic boundary conditions
>> pbc = xyz ; 3-D PBC
>> ; Dispersion correction
>> DispCorr = EnerPres ; account for cut-off vdW scheme
>> ; Velocity generation
>> gen_vel = yes ; assign velocities from Maxwell
>> distribution
>> gen_temp = 300 ; temperature for Maxwell distribution
>> gen_seed = -1 ; generate a random seed
>>
>>
>> It generates a tpr, but upon mpirun gives the following error:
>>
>> starting mdrun 'Protein in water'
>> 1000000 steps, 1000.0 ps.
>>
>> Step 0, time 0 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.027514, max 0.979682 (between atoms 3460 and 3461)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3455 3457 65.2 0.1542 0.2535 0.1526
>> 3455 3456 33.3 0.1093 0.1322 0.1090
>> 3457 3459 72.7 0.1105 0.1739 0.1090
>> 3457 3458 65.7 0.1105 0.1588 0.1090
>> 3460 3469 78.6 0.1409 0.2693 0.1400
>> 3460 3461 78.8 0.1409 0.2772 0.1400
>> 3461 3463 75.1 0.1406 0.1489 0.1400
>> 3463 3465 37.2 0.1403 0.1756 0.1400
>> 3463 3464 40.7 0.1083 0.1408 0.1080
>> 3465 3467 35.5 0.1403 0.1733 0.1400
>> 3467 3469 74.0 0.1405 0.1373 0.1400
>> 3467 3468 42.9 0.1083 0.1433 0.1080
>> Wrote pdb files with previous and current coordinates
>>
>> Step 1, time 0.001 (ps) LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 364940.065742, max 11977066.000000 (between atoms 3465 and 3466)
>> bonds that rotated more than 30 degrees:
>> atom 1 atom 2 angle previous, current, constraint length
>> 3475 3495 110.8 0.1526 20544.7148 0.1522
>> 3475 3477 111.6 0.1529 20544.4336 0.1526
>> 3475 3476 108.1 0.1094 20543.1309 0.1090
>> 3477 3480 62.8 0.1527 4.6441 0.1526
>> 3477 3479 57.5 0.1091 4.5683 0.1090
>> 3477 3478 93.6 0.1091 4.6160 0.1090
>> 3495 3497 138.1 0.1336 4.9133 0.1335
>> 3495 3496 69.6 0.1230 4.9085 0.1229
>> 3497 3499 40.2 0.1449 0.2036 0.1449
>> 3497 3498 43.8 0.1010 0.1527 0.1010
>> 3480 3483 35.6 0.1526 0.1902 0.1526
>> 3480 3482 42.2 0.1090 0.1501 0.1090
>> 3480 3481 41.7 0.1090 0.1485 0.1090
>> 3453 3455 88.7 0.1701 117322.3672 0.1449
>> 3453 3454 88.3 0.1035 65066.2227 0.1010
>> 3455 3471 48.9 0.1763 171383.6562 0.1522
>> 3455 3457 134.6 0.2535 572521.2500 0.1526
>> 3455 3456 66.7 0.1322 143042.0000 0.1090
>> 3457 3460 67.5 0.1678 877653.8125 0.1510
>> 3457 3459 126.5 0.1739 558348.5625 0.1090
>> 3457 3458 124.8 0.1588 590731.2500 0.1090
>> 3460 3469 76.0 0.2693 1002008.1250 0.1400
>> 3460 3461 72.0 0.2772 1000899.3125 0.1400
>> 3469 3470 158.0 0.1043 269832.5938 0.1080
>> 3471 3473 128.5 0.1397 181301.0469 0.1335
>> 3471 3472 107.1 0.1287 184187.9531 0.1229
>> 3473 3475 71.3 0.1467 25968.8105 0.1449
>> 3473 3474 95.3 0.1028 20024.4492 0.1010
>> 3439 3441 69.6 0.1452 7261.8906 0.1449
>> 3439 3440 61.1 0.1011 3.6659 0.1010
>> 3441 3451 75.5 0.1533 16031.6553 0.1522
>> 3441 3443 69.0 0.1529 7261.8286 0.1526
>> 3441 3442 71.2 0.1092 7260.9429 0.1090
>> 3443 3446 67.8 0.1523 4.1676 0.1522
>> 3443 3445 70.1 0.1090 4.1174 0.1090
>> 3443 3444 69.3 0.1090 4.1167 0.1090
>> 3451 3453 30.1 0.1366 48307.3984 0.1335
>> 3451 3452 76.4 0.1240 17451.3633 0.1229
>> 10016 10015 71.1 0.1410 5.2172 0.1410
>> 10017 10016 34.0 0.1090 0.1348 0.1090
>> 10036 10034 43.0 0.1090 0.1529 0.1090
>> 10035 10034 42.4 0.1090 0.1512 0.1090
>> 3461 3463 62.2 0.1489 549183.7500 0.1400
>> 3461 3462 161.0 0.1064 307931.5938 0.1080
>> 3463 3465 99.9 0.1756 1277050.1250 0.1400
>> 3463 3464 116.4 0.1408 217171.0469 0.1080
>> 3465 3467 99.6 0.1733 1273120.5000 0.1400
>> 3465 3466 79.3 0.1113 1293523.2500 0.1080
>> 3467 3469 62.5 0.1373 506361.1875 0.1400
>> 3467 3468 123.9 0.1433 186052.9531 0.1080
>> 10006 10005 118.8 0.1607 166.0911 0.1610
>> 10009 10006 107.1 0.1605 208.0792 0.1610
>> 10008 10006 93.6 0.1475 253.8065 0.1480
>> 10007 10006 89.6 0.1486 1342.3563 0.1480
>> 10010 10009 79.7 0.1420 156.5771 0.1410
>> 10013 10010 121.4 0.1526 101.7273 0.1526
>> 10012 10010 102.0 0.1091 109.8340 0.1090
>> 10011 10010 105.1 0.1090 109.8889 0.1090
>> 10032 10013 65.8 0.1528 21.9936 0.1526
>> 10015 10013 91.8 0.1411 20.4329 0.1410
>> 10014 10013 134.6 0.1092 5.6451 0.1090
>> 10037 10032 34.2 0.1410 5.9761 0.1410
>> 10034 10032 81.2 0.1526 5.9242 0.1526
>> 10033 10032 106.9 0.1090 5.9566 0.1090
>> 3446 3447 30.2 0.1229 0.1508 0.1229
>> 3437 3439 57.6 0.1336 3.7366 0.1335
>> 3437 3438 32.2 0.1229 0.1564 0.1229
>> 9980 9979 133.8 0.1410 5.2959 0.1410
>> 9986 9985 133.0 0.1410 3.7189 0.1410
>> 10002 9986 71.7 0.1527 15.9062 0.1526
>> 9988 9986 115.7 0.1475 2.9843 0.1475
>> 9987 9986 105.0 0.1090 3.0316 0.1090
>> 9989 9988 32.0 0.1365 0.1736 0.1365
>> 10004 10002 82.7 0.1091 13.0663 0.1090
>> 10003 10002 108.3 0.1092 8.0967 0.1090
>> 9983 9980 60.5 0.1529 23.4001 0.1526
>> 9982 9980 109.5 0.1091 5.3665 0.1090
>> 9981 9980 38.4 0.1091 5.2833 0.1090
>> 10000 9983 114.8 0.1527 116.4570 0.1526
>> 9985 9983 99.0 0.1412 18.6182 0.1410
>> 9984 9983 136.4 0.1091 16.0484 0.1090
>> 10005 10000 82.1 0.1424 174.5740 0.1410
>> 10002 10000 103.4 0.1527 116.8710 0.1526
>> 10001 10000 98.2 0.1091 114.7582 0.1090
>> Wrote pdb files with previous and current coordinates
>> [wagner:26697] *** Process received signal ***
>> [wagner:26697] Signal: Segmentation fault (11)
>> [wagner:26697] Signal code: Address not mapped (1)
>> [wagner:26697] Failing at address: 0xf14c110
>> [wagner:26697] [ 0] /lib64/libpthread.so.0 [0x3ae4c0eb10]
>> [wagner:26697] [ 1] mdrun_mpi [0x711b49]
>> [wagner:26697] *** End of error message ***
>> --------------------------------------------------------------------------
>> mpirun noticed that process rank 1 with PID 26697 on node
>> wagner.lbpa.ens-cachan.fr exited on signal 11 (Segmentation fault).
>> --------------------------------------------------------------------------
>>
>>
>> I am aware that the problem probably lies with LINCS algorithm, but I am
>> unsure about how to fix it.
>>
>> Any help will be greatly appreciated.
>>
>> Many thanks in advance!
>>
>>
>>
>> Rohit Arora
>> Laboratoire de Biologie et de Pharmacologie Génétique Appliquée (CNRS UMR
>> 8113)
>> Ecole Normale Supérieure, Cachan
>> France
>>
>>
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Rohit Arora
Laboratoire de Biologie et de Pharmacologie Génétique Appliquée (CNRS UMR
8113)
Ecole Normale Supérieure, Cachan
France
Bureau: +33 (0) 1 47 40 77 49
Portable: +33 (0) 6 23 85 12 46
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