Thanks Sir, I understood.. On Sat, Jun 11, 2011 at 17:30, Justin A. Lemkul <[email protected]> wrote: > > > bipin singh wrote: >> >> Dear all, >> >> I want to calculate the salt bridge interaction between a particular >> set of residues, >> because I can not use index file with g_saltbr, so the next options >> available are >> g_dist and g_mindist. As stated in manual g_dist gives the distance >> between the >> center of mass of two groups of atom, while g_mindist gives us the minimum >> distance between any pair of atom. >> My doubt is that which distance(either given by g_dist or g_mindist) >> corresponds to the salt bridge interaction distance >> between two atoms. > > Not necessarily either. g_dist measures COM distances between the given > index groups, and g_mindist measures the minimum distance of any atom pair, > which, for a multi-atom index group, may change over time. > > The solution is to create specific index groups. If you want the distance > between two specific atoms, create two index groups of one atom each and use > g_dist (or g_mindist, because in this case the output would be identical). > If you want the distance between, e.g. the amino group of lysine and the > carboxylate of glutamate, then the amine group with have four atoms (NZ, > HZ1, HZ2, HZ3) and the carboxylate group will have 3 (CD, OE1, OE2). Then > use g_dist. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 >
-- ----------------------- Regards, Bipin Singh -- 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
