[gmx-users] G_MINDIST Question

David spoel at xray.bmc.uu.se
Tue Mar 16 19:14:01 CET 2004

On Tue, 2004-03-16 at 18:48, Anthony Ivetac wrote:
> Forwarded from Katherine Cox:
> This is a general question about g_mindist with the flag option -pi
> which enables you to calulate the minium distance of a group to it's
> periodic image.
> I wanted to calculate the minimum distance between c-alpha atoms. Is the
> result I get out, the minimum distance between c-alpha atoms of the same
> residue number (i.e distance of c-alpha atom number 1 to the c-alpha
> atom of number 1 in it's periodic image) or alternatively the minimum
> distance between a c-alpha atom in one image to any calpha atom in the
> periodic image?
The latter, I assume. If you want to know the distance for the same
atom, it should be equal to the shortest box edge, unless you use a
triclinic system.

> Thanks for your help
> Katherine
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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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