On Tue, 12 Jul 2016 10:29:04 +0100 Hannes Loeffler <hannes.loeff...@stfc.ac.uk> wrote:
> On Tue, 12 Jul 2016 10:16:24 +0200 > Alexander Alexander <alexanderwie...@gmail.com> wrote: > > > Hi, > > Thanks for your response. > > I want to calculate the binding free energy of a single amino acid > > to a solid surface in aqueous solution by FEP, alchemical > > transformation, where perturbations applying on different species in > > ordered steps. For instance: Step.1 applying harmonic restraints to > > the O and H of the amino acid. Step 2. Charges removal from the > > amino acid and two water molecules and an Ion, happen. > > I think the key figure here is actually Fig. 1. What that paper > attempts to do is to replace a molecule on a surface with two water > molecules through a decoupling scheme. I guess with Gromacs you would > have to manipulate the topology files to some extent because the > decharging and recharging steps involve different species (the sodium > ion is there only to offset any changes in total charge). > couple-lamnda0/1 may be helpful for some steps. There are also both > insertions and deletions so I think step 3 must be split into two vdW > (deletion) steps. Thinking about step 3 you could probably also do it as a relative transformation i.e. omit couple-moltype and work with explicit A and B columns. -- 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.
