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

[Justin A. Lemkul]

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" <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>>
> 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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