[gmx-users] Count the number of contacts between two proteins + pbc artifacts

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jan 31 10:54:47 CET 2011

Hi Ifat,

> It seems that g_mindist is affected by the periodic boundary conditions;
> i.e. sometimes it measures the distance between one protein to the other
> that is in another frame, rather than measuring distances only between
> proteins in the same frame.

To get the number of contacts periodic images should be considered,
and not only one of them. So PBC needs to be taken into account. Why
it doesn't work out as you expect is a bit elusive as you don't
provide much information, like the command line. The only thing I can
think of is that you're molecule is broken/separated and you calculate
the distances *not* taking PBC into account. In that case you'll get
distances that are larger than they should be.



Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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