On 11/17/14 9:15 AM, behnaz abdolmaleki wrote:
Dear all I want to calculate free energy by g_lie, but I do not know how to select the length of box for free ligand simulation.should I select the dimension of box for ligand simulation (in free situation ) as same as the dimension of box in complex simulation (receptor-ligand)? or I can do whit another lenght ?
The box just needs to be large enough to avoid minimum image violations, like any other simulation; the goal there is to obtain nonbonded interaction energies between the ligand and solvent, so it's not particularly special in its setup.
-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.
