dear Justin thanks for your reply is the rerun energies needed only for protein ligand complex? do the ligand in water simulation need the rerun energies? thanks a lot
On Sunday, January 12, 2014 1:11 AM, Justin Lemkul <jalem...@vt.edu> wrote: On 1/11/14, 2:07 AM, Mahboobeh Eslami wrote: > hi dear GMX users > I simulated protein-ligand complex for 20 nanoseconds. I want to calculate > free energy by LIE method so I simulated ligand in water in the same > conditions. I used PME and full periodic boundary conditions in my > simulations so I wrote a new .mdp file that didn't use PME (I used cut off) > and used following command for protein-ligand complex simulation: > mdrun -s newtpr.tpr -rerun full20ns.xtc > then I extract -Elj and -Eqq of ligand in water simulation and use g_lie > command. > are these steps sufficient. is the stage or another commandnecessary? If the protein-ligand simulation was done with PME as well, then you need to get the rerun energies, as well. -Justin -- ================================================== Justin A. Lemkul, Ph.D. 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 ================================================== -- 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.
