Fwd: Re: [gmx-users] how to deal with large pressure fluctuation
tsjerkw at gmail.com
Wed Aug 29 14:03:19 CEST 2007
Dear Shanshan Qin,
Please keep the discussions on the list. That way, you can benefit
from the input from others as well and the discussion will be
archived. Note I didn't forward your structures/topologies, since I
don't know whether it's okay that that information is archived too...
---------- Forwarded message ----------
From: 秦姗姗 <sansanqin00 at mails.tsinghua.edu.cn>
Date: Aug 29, 2007 1:51 PM
Subject: Re: Re: [gmx-users] how to deal with large pressure fluctuation
To: Tsjerk Wassenaar <tsjerkw at gmail.com>
Thanks vey much for your kind reply. I constructed a lipid
bilayer and solvated it in the
water and energy minimized them. I ran NVT simulation using time step
0.0001 ps.After 50 ps, water
just came into the bilayer! However I can't run NPT at the very
beginning,because it would definitely
crash.I put all my input files in the attachment, will you have a look
at it?All the forcefield parameters
were downloaded from Tieleman's website.
Looking forward to your reply.
> -----Original Message-----
> From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
> Date: Wed, 29 Aug 2007 10:58:56 +0200
> To: sansanqin00 at mails.tsinghua.edu.cn,
"Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] how to deal with large pressure fluctuation
> Hi Q733,
> The large pressure fluctuation is not the cause of your problem. In
> fact, the pressure will show large fluctuations in MD anyway and this
> has been discussed on the mailing list numerous times and can be found
> on the Gromacs Wiki. That your simulation crashes is caused by
> something else, which I can not assess from the information you have
> provided. Unstable system? Not minimized enough? Overlapping atoms?
> The Fmax suggests otherwise, but something's wrong. Check your
> starting structure and your topology.
> To start with, you might want to paste your .mdp file.
> On 8/29/07, Q733 <sansanqin00 at mails.tsinghua.edu.cn> wrote:
> > Dear gmx-users:
> > I made a lipid bilayer fully hydrated by water,without water in the
> > lipid hydrophobic tails.Then I minimized the energy to Fmax=132.5,then I
> > ran NVT md for 200ps.However when
> > I wanted to run NPT simulation, the pressure fluctuation was as high as
> > 1.33*10E+05,it crashed very easily.
> > Does anyone know how to deal with large pressure fluctuation?I tried to
> > enlarge tp,however,it was of no use.
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> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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