On 1/7/17 6:05 AM, tasneem kausar wrote:
Dear all I am following Justin's tutorial methane in water for free energy calculation. I am using Gromacs-5.1.4. The charges of methane in topology are set to zero. So following the same protocol, is it relevant to set the charges at zero in topology of the drug. I am confused because in tutorial of Sander (ethanol in water) charges are present in the topology file. Please tell me the difference in both the tutorials and how can I apply it to drug that I want to study.
The charges in my tutorial are set to zero because the stated goal of that tutorial is to reproduce *only the LJ portion of the hydration free energy* to match a published paper. This creates a very simple, robust system. If you want to calculate a real, meaningful hydration or binding free energy, charge transformation is required.
-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.
