Fwd: Re: [gmx-users] how to deal with large pressure fluctuation

[Tsjerk Wassenaar]

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...

Best,

Tsjerk

---------- 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>


Dear Wassenaar:

         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.
Regards

          Shanshan Qin
> -----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.
>
> Cheers,
>
> Tsjerk
>
> 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
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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