[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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