[gmx-users] POPC Bilayer box

[David]

On Mon, 2004-04-12 at 20:23, Simon Wang wrote:
> 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.
> 
What you're doing is not scaling but increasing the system size by four.
You could also have kept the water, I don't really get why you replaced
it, but it might well be that you have a low pressure to start with 
because genbox did not fill all the holes...

So if you use anisotropic slow pressure scaling everything should be
fine. How is the density incorrect?

> Simon
> 
> >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 
> >readded
> > > 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 
> >w/
> > > pr. on the lipid. During the simulation, however, the waters at the 
> >corner
> > > of the box began to move to the middle and the density was incorrect. 
> >Please
> > > 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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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