Hi Justin, Thanks, g_dist is calculating the centre of mass of two groups and -dist option print all atoms in group 2 closer than dist to the centre of mass of group 1, while what I am looking after is the distance of COM of residues to a surface not the centre of mass of the surface. Am I missing anything? Cheers James
On Sat, Mar 28, 2015 at 1:17 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/27/15 8:03 AM, James Lord wrote: > >> Dear users, >> If I want to calculate distance of each residue's COM of a protein to a >> surface is g_mindist going to be my friend? It is documented that >> "g_mindist computes the distance between one group and a number of other >> groups. Both the minimum distance and the number of contacts within a >> given >> distance are written to two separate output files". >> > > Use g_dist, not g_mindist. > > -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 > > jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org. > -- 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.