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

Chih-Ying Lin chihying2008 at gmail.com
Sat Jan 2 21:33:59 CET 2010

As I posted the command list earlier, to create the box
editconf_mpi -f 6LYZ-EM-vacuum.gro -o 6LYZ-PBC.gro -bt cubic -d 0.75 -box
6.0 6.0 6.0

So, I think Justin's case is not the same as mine.
Thank you

Message: 1
Date: Fri, 01 Jan 2010 18:53:53 -0500
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] Simulation Box break into 16 domains =>
       Gromacs 3.3.3
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4B3E8B11.7040700 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Mark Abraham wrote:
> 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.
> Mark
I have a strong suspicion that this all derives from the incorrect editconf
command posted earlier.  I saw something like this once, long ago, before I
what I was doing :)  The problem I had stemmed from incorrectly assigning
center of the system.
I would suggest re-building the system, starting from the editconf step, and
centering the protein with -c in a box defined *either* by -d or -box, to
see if
that fixes things.
> ------------------------------------------------------------------------
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