[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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