[gmx-users] POPC Bilayer box

Simon Wang sim_wang03 at hotmail.com
Mon Apr 12 20:24:01 CEST 2004

Hello, David:

I used either
'genconf -f popc.gro -o popc4n.gro -nbox 2 2 1'
or 'genconf -f popc.gro -o popc4n.gro -trj popc200ps.trr -nbox 2 2 1'

The version I used is GMX3.2.1. Please let me know if I missed anything or 
there is better way to scale the box size. Thanks a lot.


>From: David <spoel at xray.bmc.uu.se>
>Reply-To: gmx-users at gromacs.org
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] POPC Bilayer box
>Date: Mon, 12 Apr 2004 07:45:55 +0200
>On Mon, 2004-04-12 at 08:21, Simon Wang wrote:
> > Dear gmx-users,
> >
> > I started from Peter's popc128a.pdb and extended the z dimension and 
> > water. The system was stable in 200ps w/ PME. Then I scale the box size 
>to a
> > larger one by genconf. The new system was fully minimized and run 50ps 
> > pr. on the lipid. During the simulation, however, the waters at the 
> > of the box began to move to the middle and the density was incorrect. 
> > enlighten me the reason for this and the possible solutions.
> >
>more details please, what did you do with genconf?
> > Thanks in advance,
> >
> > Simon
> >

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