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

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Aug 29 10:58:56 CEST 2007

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

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