[gmx-users] Mdrun error

Mark Abraham Mark.Abraham at anu.edu.au
Tue Aug 25 23:56:37 CEST 2009

Cíntia C. Vequi-Suplicy wrote:
> Hello Justin,
> I used Gromacs 4.0.5 and the error was gone. Thank you.
> But now I have another problem when using mdrun_d. I gave the comand:
> mdrun_d -s dppc.tpr -o dppc128.trr -c dppc128.gro -g dppc.log  &
> And first I got  a lot of output on the shell window and I think it is 
> strange. This output should be on a file or not?

No, this output to stdout is normal. 3.3.3 does that too. Roughly the 
same content got written to the .log file. It sounds like you should do 
some tutorial material to get used to the GROMACS workflow.

> And  after a few seconds I got an error which says:
> t = 0.052 ps: Water molecule starting at atom 17276 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> Back Off! I just backed up step26b.pdb to ./#step26b.pdb.2#
> Back Off! I just backed up step26c.pdb to ./#step26c.pdb.2#
> Wrote pdb files with previous and current coordinates
> MPI process rank 0 (n0, p23764) caught a SIGSEGV.


You should do some searching on the wiki/web to help diagnose your own 
problems before asking here :-) You'll learn more about problems you've 
solved yourself :-)


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