[gmx-users] POPC Bilayer box
spoel at xray.bmc.uu.se
Mon Apr 12 21:06:02 CEST 2004
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?
> >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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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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