On 10/15/14 2:19 PM, Diogo Martins de Sá wrote:
Fellow users, I have read several emails exchanged in this discussion list where g_dist is presented as a better choice for observing salt bridges in the trajectory. And I'm totally inclined to agree with that, but that would be the case where you already know which are the SBs present in the system. If one has this information, he could easily create groups of individual residues (which would actually contain just the ionazable atoms and their hydrogens, depricating the carbons and other atoms) and observe how the salt bridges behave. My question is concerning the situation where you still don't know which are the salt bridges in the system and, after that, which are the ones you should take a closer look (I think the obvious approach would be to search literature, but that is not always successful). Justin Lemkul has mentioned, in two diferent discussions, using g_dist to "track persistence of interactions" and "looping calculations" to address the situation I've just mentioned. Could someone elaborate on those? I am confused as to what they actually mean and how to proceed (especially in the case of "looping calculations").
Likely I was referring to looping over calls to g_dist (in the future, please link to any previous discussions - it's hard for me to keep track of all of the thousands of messages I've sent :)
One can certainly use g_saltbr to look at positive-negative interactions en masse, but it's a fairly "dumb" program, in that it considers a huge amount of groups that don't matter. You can weed through all of that to find things that might be of interest.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [email protected] | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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 [email protected].
