[gmx-users] negative pressures!
Mungikar, Amol Arvind (UMR-Student)
mungikar at umr.edu
Wed Feb 25 07:40:01 CET 2004
Thank you very much for your suggestions, infact things are working fine for me now with NPT ensemble.
From: gmx-users-admin at gromacs.org on behalf of Eric Jakobsson
Sent: Sun 2/22/2004 9:18 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] negative pressures!
That sounds to me like normal behavior. For a small system the
instantaneous pressure fluctuations are enormous, of the order you are
seeing. Furthermore, water is almost incompressible, so if you do NVT at a
density that is just a little bit off the density you would have for a 1
atm NPT simulation, you will have an enormous net pressure, either positive
or negative depending on whether your density is just a little too big or a
little too small.
Why not run NPT, so the system finds its own appropriate density?
At 09:44 AM 2/19/2004 -0600, you wrote:
>I posted a similar message few days back, and since then I am trying to
>find out where the bug is! I ran NVT md simulations for water,
>peptide-water. And everytime for this NVT ensemble run, I am getting
>pressures +/- 1000 bars. Dr.Spoel mentioned that this might be because of
>a 'air bubble' in the system, or based on previous discussions in this
>forum it maybe due to the high (wrong) densities. I checked the density
>value (1 gm/cm3) for water box several times. I checked all the RDFs but i
>couldnt locate anything wrong here. I am sure that I am missing out
>something, but sadly i dont know what. Kindly help me out in this
>matter.Thank you very much in advance.
Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
405 N. Mathews Avenue
University of Illinois, Urbana, IL 61801
ph. 217-244-2896 fax 217-244-2909
(Currently on leave to NIH to serve as Director of Center for
Bioinformatics and Computational Biology at the National Institute of
General Medical Sciences and Chair of the NIH Biomedical Information
Science and Technology Initiative Consortium. Usual schedule is four days
a week at NIH and three days a week at Illlinois.)
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