[gmx-users] Fwd: thanks very much, I know where I am wrong

[Tsjerk Wassenaar]

---------- Forwarded message ----------
From: 秦姗姗 <sansanqin00 at mails.tsinghua.edu.cn>
Date: Aug 30, 2007 3:12 AM
Subject: thanks very much, I know where I am wrong
To: Tsjerk Wassenaar <tsjerkw at gmail.com>


Dear Wassenaar:

            I know why my NPT simulation always crash: I made a very
stupid mistake, I used position restriction
to the P atom of the lipid,and semiisotropic pressure coupling with a
Z coupling compressibility of
1e-5. Can I ask you a question: if we use semiisotropic  pressure
coupling method to simulate lipid,what
should the Z compressibility be? Should it be zero?

            Thanks again for your willing to help

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 yourp
> 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