Sir, I thought that the order should not matter but when I used 18 - 1 and 1 - 18 the graph were slightly off.
Group 18 is a set of residues in that protein with some unique property. I wanted to see the variation of Hbond of these residues with the whole protein. so group 18 is a subset of group 1. Thank you Kavya On Wed, Dec 19, 2012 at 10:06 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/19/12 9:37 AM, Kavyashree M wrote: > >> Dear users, >> >> While using g_hbond, does it make any difference if I give option >> 18 and 1 or 1 and 18? >> > > Order does not matter. > > > I wanted to find the hydrogen bonding of a group of residues with >> the whole protein so I had an index of this group. When I give the >> option as 18 (index number) and 1 (whole protein), I get several >> messages >> "Hm. This isn't the first time I found this donor (...,...)" >> But later it does calculates. does this mean that it is double counting >> those interactions? >> >> > What is group 18? Be mindful of the g_hbond requirement that the chosen > groups must be completely unique or completely overlapping. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists