On 12/1/16 9:17 PM, Mijiddorj Batsaikhan wrote:
Dear gmx_users, I started simulation that a peptide on membrane. My peptide locates on the membrane surface. I have two questions relating to the simulation. (1) When I start the simulation, I chose COM groups separately. Is this choice okay? or May I need to chose COM group inseparately?
Your description is ambiguous; please post the actual .mdp contents.
(2) During the simulation peptide is moving the edge of membrane. How can I shift the peptide to the central section of the membrane? Can I use -nojump, -center options of trjconv tool?
Yes - try it and see. Also relevant is -fit transxy. -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.
