[gmx-users] MD continuation runs in serial but not in parallel

[Sridhar Acharya]

Dear GMX users,
I used grompp with -t option to continue a serially run simulation to 
run in parallel. I have given gen_vel = no in the .mdp file.
But mdrun "with -np 2" stops and reports the following error. (md.log 
file is given below)
The same simulation could be continued in serial without any error.
What is the cause for this descrepancy? Any parameters to be set?
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Going to use C-settle (5335 waters)
wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.081665, ra = 0.00645837
rb = 0.051255, rc2 = 0.16333, rone = 1, dHH = 0.16333, dOH = 0.1

Constraining the coordinates at t0-dt (step -1)
   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.000042   4862   4887   0.000007
        After LINCS         0.000049   4880   4881   0.000010

Started mdrun on node 0 Mon Jul  3 18:48:47 2006
Initial temperature: 301.39 K
Grid: 17 x 14 x 19 cells
           Step           Time         Lambda      Annealing
              0        0.00000        0.00000        1.00000

   Rel. Constraint Deviation:  Max    between atoms     RMS
       Before LINCS         0.058480   3573   3574   0.005918
        After LINCS         0.000140   3842   3844   0.000020


t = 0.000 ps: Water molecule starting at atom 17176 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous and current coordinates
   Energies (kJ/mol)
       G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    8.10484e+03    3.58568e+03    2.61866e+03    1.41412e+03    4.86285e+04
        LJ (SR)   Coulomb (SR)   Coulomb (LR)      Potential    Kinetic En.
    2.14166e+08   -5.54411e+05   -1.31762e+05    2.13544e+08            nan
   Total Energy    Temperature Pressure (bar)
            nan            nan            nan
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-- 
Sridhar Acharya, M
Senior Research Fellow
Lab of Computational Biology
CDFD, Gandipet Campus
Hyderabad. AP. INDIA
http://www.cdfd.org.in
email: sridhar at cdfd.org.in
Phone: Lab: 08413-235467*2044
Mobile: 9866147193


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