On 8/18/14, 10:06 AM, Mahboobe Sadr wrote:
Dear all, I am new in gromacs and specially in MD simulation of membrane protein, in part "define box and solvent" of justin's tutorial , in scaling down the lipids, I reached an area per lipid of ~69 A^2, after 4 times instead of 26 times.... I don't know ,where I made a mistake?
Without seeing your exact commands and the corresponding output, there's nothing to say. If you scale each time by 0.95, it is mathematically impossible to arrive at a proper APL in this system with only 4 iterations. At least one of your commands or preparation steps was wrong; the outcome is extremely reproducible.
-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 [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].
