On 9/18/14 2:04 PM, Carlos Navarro Retamal wrote:
Dear gromacs users, In order to measure the interactions between a Protein with respect to a mixture solvent solution (glycerol-water) i’m trying to measure the RDF between the protein with respect to the C and O atoms of Glycerol respectively. By now i have measured g(r) between: Protein - Glycerol Protein Backbone - Glycerol SideChain - Glycerol but sadly, because i’m considering a huge amount of atoms of the Protein, the RDF graphic doesn’t look that good. On that way i thought that maybe a better approximation will be to measure the RDF between the center of Mass of the protein with respect to the glycerol molecules, but i don’t know how to use make_ndx to create such kind of group.
It's not a task for make_ndx. g_rdf does this with the -com option. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
