Hi, To what end? These are non-physical states.
Mark On Sun, 11 Jun 2017 16:28 Varvdekar Bhagyesh Rajendra < bhagyesh.varvde...@research.iiit.ac.in> wrote: > Dear Justin, > > Thank you for the valuable insight. > > While on the same subject, can you give any comments on the possibility of > using the same Free energy code in Gromacs to scale the non bonded > interactions between protein & ligand while simultaneously doing Normal > Mode analysis on the scaled interaction conformation to study the effect of > the scaled interactions. > > If its not plausible in Gromacs, can you suggest any other software. > > Best Regards, > > Bhagyesh > > ----- Original Message ----- > From: "Justin Lemkul" <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Sent: Sunday, June 11, 2017 7:01:26 AM > Subject: Re: [gmx-users] Doubt about Free Energy Calculations using g_bar > > On 6/10/17 6:15 AM, Varvdekar Bhagyesh Rajendra wrote: > > Dear Justin, > > > > Just so we are on the same page, this means that if I don't touch the > topology file and use the following mdp snippet, charges *are present* in > the topology file for the ligand group and they are automatically set to > zero while turning on vdW interactions (from 0 to 1) right ? Hence, there > is no need to manually set charges to zero (The old style of doing the > calculations), right?. > > > > Yes. You can easily confirm this using energygrps between your transformed > molecule and the rest of the system. Coul-SR should be zero. > > > Then the charges too, are turned off from 0 to 1? (1 state being the > actual charges present in the topology file). > > > > Charges are turned *on* if they are defined as off in the A-state > (lambda=0) and > on in the B-state (lambda=1). > > -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. > -- > 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. > -- 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.