On 5/31/14, 5:40 AM, Mahboobeh Eslami wrote:
dear justin I sincerely thank you for your good adviceI have done all the steps that you've said. if I use α=0.181 and β=0.5 , the free energy calculation results will be very different from the experimental values But if i use α=0.5 and β=1.043 (According for results Aqvist et al 1994, 1998) , the results will close to the experimental values. What suggestions do you have for the α,β and γ parameters?
Whatever you can justify based on robust, published protocols. AFAIK values for those fitting parameters are somewhat system-dependent.
-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 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.
