[gmx-users] contact

[Erik Marklund]

Well, one way is to use g_hbond -contact. It will give you the number of
contacts each frame plus some additional information, if that's what
you're after. Make sure you use the cvs version of g_hbond, since
previous versions did not handle contacts correctly (for some reason,
most of my replies on this list seem to end in that very sentence).

On Mon, 2006-08-14 at 06:06 -0700, mahbubeh zarrabi wrote:
> Dear gromacs users
> How can i calculate the number of contacts during the
> MD trajectory in complex(protein-protein)?
> best regard
> 
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-- 
Erik Marklund, PhD Student, Molecular Biopcysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone: +46 18 471 4537          fax: +46 18 511 755
erikm at xray.bmc.uu.se