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

[Mark Abraham]

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.

Mark