[gmx-users] Re: NVE problems
David van der Spoel
spoel at xray.bmc.uu.se
Sun Dec 28 14:59:01 CET 2003
On Sun, 28 Dec 2003 istvan at kolossvary.hu wrote:
>Thanks for the hints and the reference. I am using SPC water and I suppose I
>use settle, because the error message says that some water could not be
>settled. However, I don't know how to "settle" explicitly. I may have
>overlooked it, but I don't seem to find anything about settle in the manual.
settle is analytically correct solution of the constraint problem. For the
protein to conserve energy you need double precision, a short time step
with bonds or use shake with reduced tolerance (1e-8) or linc with higher
lincs order. Even then there is roundoff error, accumulating as noise
(i.e. heating). Some of this noise can be compensaed for by setting
nstlist > 1, and hence making a small error in the Van der Waals energy,
leading to cooling...
Maybe someone out there can volunteer to write a NVE Howto...
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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