dear justin I sincerely thank you for your answer my questions I saw the following description for tpbconv command in the gromacs manual: "by setting the charges of a specified group to zero. This is useful when doing free energy estimates using the LIE (Linear Interaction Energy) method". I do not know how to use this command.I think that this command is used only for charged ligand. is this correct? Thanks and best wishes
On Sunday, January 12, 2014 7:19 PM, Justin Lemkul <jalem...@vt.edu> wrote: On 1/12/14, 12:03 AM, Mahboobeh Eslami wrote: > 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? Both. It wouldn't make sense to re-calculate energies from one PME system, then try to take the difference of the energies from another system where the same correction hasn't been applied. -Justin > 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 <mailto:jalem...@outerbanks.umaryland.edu> | > (410) 706-7441 > > > ================================================== > > -- ================================================== 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_Listbefore 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-usersor send a mail to gmx-users-requ...@gromacs.org. -- 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.
