Hi, 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. Thanks, Ifat
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