[gmx-users] gromacs error

[Justin Lemkul]

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

==================================================