Hi, The usual way is to build a topology whose A and B states are the mutated forms, and you then equilibrate the system separately at each lambda point interpolating between them. You "simply" need a starting configuration with a plausible geometry for each such point.
Mark On Mon, Feb 15, 2016 at 9:27 PM Jagannath Mondal <jmondal.bac...@gmail.com> wrote: > Dear Users > I want to compute the relative free energy for mutating one residue of a > protein to another one using free energy perturbations as implemented in > gromacs. I wanted to know how I can generate the starting configurations of > the intermediate lambda values. Is there any interpolation scheme within > gromacs that will let me generate the intermediate structures. > Jagannath > -- > 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.
