[gmx-users] Microcanonical

David van der Spoel spoel at xray.bmc.uu.se
Mon May 22 14:40:11 CEST 2006

A B wrote:
>> Please refer to my recent paper, J. Chem. Theor. Comp. 2 (2006) 1-11.
> Yes, this is exactly what I mean - an appropriate smoothing function 
> ("shift") works fine, but simple group-based truncation does not; that 
> this does not work has indeed been known since long before GROMACS was 
> born. Maybe the "NVE cutoff" issue is merely semantic, where cutoff 
> should be interpreted in a slightly restricted sense as "spherical 
> cutoff method using group-based truncation"?
You should use neither, at least not for Coulomb. Only PME can be used 
for systems containing charges. For system containing exclusively 
neutral molecules, you can use a shift function, if the cut-off is 
longer than the range of the interaction. For water that would be 
roughly 1.2 nm.

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David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se

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