Have you had a look at http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme
to see if that technique would be applicable to you and look through the references given? When you do absolute transformations you will need to think about standard state (and standard volume). On Thu, 13 Oct 2016 15:33:47 +0200 Alex <alexanderwie...@gmail.com> wrote: > Dear gromacs user, > > As you know the binding free energy is the difference between the free > energy change inbounded state and unbounded state. > > \Delta (\Delta G)_(binding) = \Delta G_(bounded) - \Delta > G_(unbounded). > > Then my question is that if it is necessary to simulate the free > energy change of bonded and unbounded states in the identical volume > size? > > In another meaning if the free energy change (either bounded or > unbounded) is a volume depended quantity? > > I am using FEP method to calculate the binding free energy of amino > acid to a solid surface. > > Best regards, > Alex -- 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.
