[gmx-users] gromacs error

Urszula Uciechowska urszula.uciechowska at biotech.ug.edu.pl
Thu Jul 31 14:16:37 CEST 2014


How should I correct the input file?

Urszula Uciechowska
>
>
> On 7/31/14, 7:42 AM, Urszula Uciechowska wrote:
>> Dear Gromacs users,
>>
>>
>> I tried to run coarse grained MD however after a few steps I got:
>> Step 39, time 0.78 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 0.038933, max 2.260527 (between atoms 10459 and 10463)
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>>    10457  10459   89.8    0.3107   0.8288      0.3100
>>    10459  10463   90.3    0.3075   1.0108      0.3100
>>    10463  10467   90.6    0.3084   0.8774      0.3100
>>    10467  10469   81.1    0.3103   0.3823      0.3100
>>    10469  10471   90.3    0.3121   0.1885      0.3100
>> Wrote pdb files with previous and current coordinates
>>
>> Step 40, time 0.8 (ps)  LINCS WARNING
>> relative constraint deviation after LINCS:
>> rms 165002.767686, max 10334958.000000 (between atoms 10457 and 10459)
>> bonds that rotated more than 30 degrees:
>>   atom 1 atom 2  angle  previous, current, constraint length
>>    10443  10445   30.1    0.3100   0.3581      0.3100
>>    10445  10447  102.2    0.3102 266.6146      0.3100
>>    10447  10450   59.3    0.3100 624.1382      0.3100
>>    10450  10452  101.4    0.3105 5390.4609      0.3100
>>    10452  10454   87.9    0.3083 104154.3047      0.3100
>>    10454  10457   83.9    0.3497 439143.5312      0.3100
>>    10457  10459   87.5    0.8288 3203837.2500      0.3100
>>    10459  10463   87.8    1.0108 2960821.2500      0.3100
>>    10463  10467   95.2    0.8774 763857.8125      0.3100
>>    10467  10469   95.5    0.3823 195859.2656      0.3100
>>    10469  10471  104.3    0.1885 43565.4141      0.3100
>>    10471  10473   90.3    0.3534 7857.3394      0.3100
>>    10473  10475  105.5    0.3125  57.7529      0.3100
>>    10475  10477   90.0    0.3099   0.3849      0.3100
>>    10477  10480   32.4    0.3101   0.3647      0.3100
>> Wrote pdb files with previous and current coordinates
>> mpiexec: process_obit_event: evt 6 task 0 on wn518 stat 267.
>> mpiexec: wait_tasks: waiting for wn350 wn350 wn501.
>> mpiexec: kill_others_now: alarm went off, killing all other tasks.
>> mpiexec: kill_tasks: killing all tasks.
>> mpiexec: process_kill_event: evt 10 task 1 on wn350.
>> mpiexec: process_kill_event: evt 12 task 3 on wn501.
>> mpiexec: process_kill_event: evt 11 task 2 on wn350.
>> mpiexec: process_obit_event: evt 7 task 3 on wn501 stat 265.
>> mpiexec: process_obit_event: evt 8 task 1 on wn350 stat 265.
>> mpiexec: process_obit_event: evt 9 task 2 on wn350 stat 265.
>> mpiexec: Warning: task 0 died with signal 11 (Segmentation fault).
>> mpiexec: Warning: tasks 1-3 died with signal 9 (Killed).
>>
>> in log file last line is:
>>
>> Constraining the starting coordinates (step 0)
>>
>> Constraining the coordinates at t0-dt (step 0)
>> RMS relative constraint deviation after constraining: 4.04e-06
>> Initial temperature: 1.8161e-07 K
>>
>> Started mdrun on node 0 Wed Jul 30 10:39:50 2014
>>
>>             Step           Time         Lambda
>>                0        0.00000        0.00000
>>
>> Grid: 42 x 42 x 42 cells
>>     Energies (kJ/mol)
>>             Bond       G96Angle    Proper Dih.  Improper Dih.        LJ
>> (SR)
>>      6.24872e+03    1.47844e+04    1.75778e+03    4.11810e+02
>> -2.32179e+07
>>     Coulomb (SR) Position Rest.      Potential    Kinetic En.   Total
>> Energy
>>     -4.49776e+03    2.00073e-01   -2.31992e+07    1.44043e+01
>> -2.31992e+07
>>      Temperature Pressure (bar)   Constr. rmsd
>>      1.55259e-03   -1.41563e+03    5.56533e-06
>>
>> my input file:
>>
>> define           =  -DPOSRES
>> dt               =  0.02
>> nsteps           =  25000
>> nstxout          =  0
>> nstvout          =  0
>> nstlog           =  100
>> nstxtcout        =  100
>> xtc-precision    =  10
>> rlist            =  1.4
>> coulombtype      =  shift
>> rcoulomb         =  1.2
>> epsilon_r        =  15
>> vdw-type         =  shift
>> rvdw-switch      =  0.9
>> rvdw             =  1.2
>> tcoupl           =  v-rescale
>> tc-grps          =  Protein W
>> tau-t            =  1.0 1.0
>> ref-t            =  300 300
>> Pcoupl           =  Berendsen
>> Pcoupltype       =  isotropic
>> tau-p            =  12.0
>> compressibility  =  3e-4
>> ref-p            =  1.0
>> refcoord_scaling =  com
>>
>>What is wrong here?
>>
>
> Likely this:
>
> Initial temperature: 1.8161e-07 K
>
> You haven't generated any velocities, so your system is effectively
> frozen, and
> you're simultaneously applying a thermostat and barostat, which probably
> cause
> your velocities to go absolutely insane, blowing up the system.
>
> Generate velocities at the desired temperature and equilibrate gently.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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