[gmx-users] Re: Simulation Box break into 16 domains => Gromacs 3.3.3
Justin A. Lemkul
jalemkul at vt.edu
Sat Jan 2 21:41:16 CET 2010
Chih-Ying Lin wrote:
> 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.
Mark already pointed out that your command line is malformed. You cannot use -d
and -box simultaneously. They are mutually exclusive. You are also not
centering the protein in the box (you are not using the -c option). So, in
fact, what you're doing was exactly what my problem was - not centering and
potentially defining the box incorrectly.
I would suggest that you at least try rebuilding your system, because the above
command is certainly wrong.
> Thank you
> Message: 1
> Date: Fri, 01 Jan 2010 18:53:53 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto: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
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4B3E8B11.7040700 at vt.edu <mailto:4B3E8B11.7040700 at vt.edu>>
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> 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.
> 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 knew
> what I was doing :) The problem I had stemmed from incorrectly
> assigning the
> 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.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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