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

ifat shub shubifat at gmail.com
Mon Jan 31 10:46:45 CET 2011


I would like to count the number of contacts between two proteins.

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.

I tried using the –pbc options but it didn’t seem to help.

Any suggestions on how to force the g_mindist to consider only contacts  that
take place in the same periodic frame.


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