Thanks for your reply. But would you please tell me what is known for the pull_group line? I mean are the atom names or resid-s or residue names or .... know for it?
Sincerely, Shima ----- Forwarded Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Tuesday, July 16, 2013 3:39 PM Subject: Re: [gmx-users] make an index file of COM of lipid bilayer On 7/16/13 5:30 AM, Shima Arasteh wrote: > > > Hi, > > > Would you please let me know how can I make an index file of COM of lipid > membrane? > I guess the position of the COM of the bilayer, but how it is possible to > make an index file of this point? > > I want to include this index file as the ref_group in Umbrella Sampling. > Index files can't specify positions, only atoms. In this case, you don't even need a special index group - just use the membrane. The pull code uses the COM of the selected group, so if you specify your membrane, mdrun knows to use its COM. -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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- 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
