Thank you Justin... that's what I was looking for ...
On Tue, Nov 19, 2013 at 2:24 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > 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 gromacs.org_gmx-users@ > maillist.sys.kth.se > 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 > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.