[gmx-users] restarting jobs

Martina Bertsch, PhD mbe404 at lulu.it.northwestern.edu
Wed Mar 10 23:16:01 CET 2004

Try minimization of your system or delete the problematic water molecule.


Marc Vogt wrote:

>I'm having a problem restarting mdrun jobs that had to be killed
>prematurely.  I am using the procedure suggested on the web site:
>tpbconv -s test.tpr -f test.trr -e test.edr -o test2.tpr
>When I restart the job using test2.tpr, it dies almost immediately
>with the following error:
>t = 24800.033 ps: Water molecule starting at atom 17397 can not be settled.
>Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates
>Large VCM(group rest): -9130668912982097920.00000, 56782976194724233216.00000, -34004343224553963520.00000, ekin-cm:          inf
>Fatal error: ci = -2147483648 should be in 0 .. 511 [FILE nsgrid.c, LINE 218]
>This happens for two trajectories independent of whether or not I
>specify a different frame for tpbconv with the -time option.  And it
>is also independent of whether or not I specifiy the energy file.
>I tried to make a .gro file using trajectory convert so that I could
>modify the .mdp file to reduce the timestep (2fs to 1fs) and got essentially the same error.
>As far as checking for bad contacts, I'm not sure how to do this,
>but it seems strange that both trajectories would have bad contacts
>at whatever restart point I choose.
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