[gmx-users] Is there any problem of pme in GROMACS3.3?

Mark Abraham Mark.Abraham at anu.edu.au
Mon Mar 6 20:26:45 CET 2006

Sui Shen wrote:
> Dear All! I have 2 questions:
> I tried to use PME (order: 6) for my simulation, but it always exploded. 
> When I changed PME to Cut-off, it was OK. Is there any problem about PME 
> in GROMACS3.3?

Yes. There was a bug in the distribution version of 3.3 for order != 4.
See http://www.gromacs.org/pipermail/gmx-users/2005-November/018047.html
and thread for info and fix.

> In addition, is there any differences between GROMACS-parallel (many 
> processors) and GROMACS-local? I tried a 1ps simulation by using my 
> local machine, and that was fine. However, The system exploded when I 
> used parallel GROMACS as totally the same environment and parameters.

You just need to invoke grompp with the right parameters, and mpirun
mdrun with the right parameters. Read the manpages.


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