On 2/10/14, 3:59 PM, shivangi nangia wrote:
Dear Gromacs users, I have a question regarding the input file group.dat that has to be supplied for using g_enemat. The manual says "With *-groups* a file must be supplied with on each line a group to be used." I need to calculate the interaction energy of each of my protein residue (186 residues) with only tail groups of the bi-layer. I am not sure what exactly to write in the group.dat file: residue numbers? atom/bead (CG) name? Will it use the groups I had in the index file that were incorporated in the .edr file?
What you need are energygrps in the .mdp file. g_enemat is only a post-processing tool for existing energygrps; it cannot decompose nonbonded interactions in the way that you want.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. 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 [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].
