Chih-Ying Lin wrote:
Hi
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.
-Justin
Thank you
Lin
Message: 1
Date: Fri, 01 Jan 2010 18:53:53 -0500
From: "Justin A. Lemkul" <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] Simulation Box break into 16 domains =>
Gromacs 3.3.3
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <4b3e8b11.7040...@vt.edu <mailto:4b3e8b11.7040...@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 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
------------------------------------------------------------------------
--
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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