[gmx-users] opteron, 64bit

David spoel at xray.bmc.uu.se
Tue Jan 6 20:33:00 CET 2004

On Tue, 2004-01-06 at 20:21, Ilya Chorny wrote:
> Has anyone hacked gromacs such that the cutt-off distance is always half
> the boxlength?

you mean when the box-length changes? I don't think so.
Further I'm not sure if it is desirable: look at the following example

|                      |
|WAT        WAT        |
|                      |

If the cut-off is shifted by an infitesimal amount the water in the
center can suddenly see the other image of the water on the edge. This
may lead to noise (not sure though...). I'd want the cut-off to be at
most half the box minus the charge group size (for water 2 Å).

Testing might be useful though...

> Thanks
> Ilya
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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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