[gmx-users] restarting jobs

Marc Vogt mvogt at es.chem.umass.edu
Wed Mar 10 18:13:01 CET 2004


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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