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. Cheers, Tsjerk -- 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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
