On 12/29/14 6:28 AM, h.aliza...@znu.ac.ir wrote:
Dear Users, I am simulating a membrane protein with charmm ff with a 2fs time step. How the results will be affected if I use a 5fs time step by using "-vsite hydrogen" option in pdb2gmx? Do my results loose their accuracy if I use this option?
Well, it's easy to test. The membrane properties that are expected to be observed are very easy to quantify. We didn't test our CHARMM36 port with virtual sites at all, so we cannot recommend such usage. Test thoroughly before doing any real production work. Membranes are extremely sensitive to alteration.
-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.
