On 11/14/13 10:18 PM, bharat gupta wrote:
Hi, How can I calculate the average number of salt bridges between two residues during the entire simulation ??...
Unless you've got some wildly noncanonical residues, this is a binary function. Either the salt bridge exists (1) or does not (0). You can define a salt bridge a number of ways, but the easiest and most common is the distance between the COM of the positive and negative moieties. Use g_dist over time and post-process the output to determine the fraction of time spent within the distance cutoff; it's a much more useful quantity.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- gromacs.org_gmx-users mailing list email@example.com https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists