[gmx-users] Simulation Box break into 16 domains => Gromacs 3.3.3

Mark Abraham Mark.Abraham at anu.edu.au
Sat Jan 2 00:44:57 CET 2010

Chih-Ying Lin wrote:
> Hi
> Sorry that i have posted the same message for several times.
> I used Gromacs version 3.3.3.
> My simulation system = one protein + 20 ligand + water molecules ( 7x 7x 7
> )
> MPI setting => #PBS -l nodes=4:ppn=4,arch=x86_64   => 16 nodes in total
> After doing the energy minimization, => the potential energy is extremely
> high ( say, ten to the 9th order )
> I visualized the " Simulation-System-EM-solvated.gro " after the energy
> minimization.
> Then, I found that the Simulation Sysmtem is devided into 16 domains very
> clearly and the molecules (protein, ligand, and water) break into atoms in
> the boundaries.
> I have checked that the 20 ligands are not overlapped each other and are not
> overlapped with protein from the beginning.

Chih-Ying sent me before and after .gro files off-list, and the
structure really has done something like this (pic attached). After EM,
the cubic simulation cell has partitioned four times along each side,
and within each small cube, the waters have contracted as if to minimize
surface area. The result is as if each small cube did an EM in isolation
of any other such cube.

Are you sure you are using a 3.3.3 mdrun? Consult the top part of the
log file. I'd guess the most likely problem is that you're seeing some
bizarre artefact of your MPI or installation. How was GROMACS
configured? Did you use shared libraries? Try a version without. Try
single-processor grompp+mdrun.

If there's no light shed by the above, please send me your input protein
and ligand structure files, and your pre-EM .tpr and I'll see if I can
reproduce your workflow or result.


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