On 11/13/14 4:09 AM, RINU KHATTRI wrote:
hello gromacs users i am working on protein ligand complex with popc membrane i want to calculate the free energy of protein and ligand i have to follow which tutorial (methane in water) but my protein is membrane protein i am also running md simulation (70 ns) i am new in free energy calculation from where i have to start after the production md or i can start from the original pdb file
The "free energy of protein and ligand" is a rather ill-defined quantity. Are you trying to calculate binding free energy? If so, there's a huge amount of literature on this topic. It comes down to simply doing a thermodynamic cycle of the ligand in water and in the binding site. Restraints might be needed to keep the ligand bound while being decoupled, but again there's tons of papers on this topic.
-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.
