[gmx-users] NVE problems
jake at ncsa.uiuc.edu
Sun Dec 28 00:09:01 CET 2003
See Chiu, S.-W., Clark, M., Subramaniam, S., and E. Jakobsson. 2000.
Collective motion artefacts arising in long-duration molecular dynamics
simulations. J. Comp. Chem. 21:121-131 For a description and discussion
of this type of phenomenon.
At 06:47 PM 12/27/2003 +0100, you wrote:
>I posted a message right before Christmas (gmx-users digest, Vol 1 #1166)
>about problems with NVE. I have a feeling that the nsgrid error that I
>mentioned is not specific to the problem, it just shows a general
>numerical instability due to the NVE simulation. In other cases Gromacs
>blows up with other numerical errors. In any case, I guess the simplest
>way to present the problem is to ask why should Gromacs blow up on alanine
>dipeptide in a 3x3x3 nm box using NVE instead of NPT? I can hardly think
>of anything simpler. The system was minimized, PR-equilibrated (FF was
>OPLS-AA), but then a fully unconstrained run with PME that would normally
>run without problems in NPT, blows up after only 1 ns using a 1 fs time
>step when I turn off temperature and pressure control. Shouldn't a 1 fs
>time step be adequate for NVE without LINCS/SHAKE? Can anyone experienced
>with NVE in Gromacs help me?
> Istvan Kolossvary _______________________________________________
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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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