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

[Berk Hess]

>From: Sridhar Acharya <sridharfirst at gmail.com>
>Reply-To: sridhar at cdfd.org.in,Discussion list for GROMACS users 
><gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] MD continuation runs in serial but not in parallel
>Date: Mon, 03 Jul 2006 17:56:27 +0530
>
>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?
>#########################################################################################
>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
>##############################################################################################
>
>--

Did you use the -shuffle option of grompp?
With grompp -shuffle -t
grompp expectes a shuffled trajectory.

Berk.