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. 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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