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See <font face="MS Serif, Geneva">Chiu, S.-W., Clark, M., Subramaniam,
S., and E. Jakobsson. 2000. Collective motion artefacts arising in
long-duration molecular dynamics simulations. <i>J. Comp.
Chem. </i>21:121-131 For a description and discussion of this type of
phenomenon. <br><br>
<br>
</font>At 06:47 PM 12/27/2003 +0100, you wrote:<br>
<blockquote type=cite class=cite cite>Hi, <br>
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? <br>
Many thanks, <br>
Istvan Kolossvary
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</blockquote>
<x-sigsep><p></x-sigsep>
---------------------------------<br>
Eric Jakobsson, Ph.D.<br>
Professor, Department of Molecular and Integrative Physiology, and of
Biochemistry<br>
Senior Research Scientist, National Center for Supercomputing
Applications<br>
Professor, Beckman Institute for Advanced Science and Technology<br>
4021 Beckman Institute, mc251<br>
405 N. Mathews Avenue<br>
University of Illinois, Urbana, IL 61801<br>
ph. 217-244-2896 fax
217-244-2909<br><br>
(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.)<br><br>
<br>
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