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. Probably best to work this out by going through steps 1 to 6 an pay careful attention to what species have zeroed out charges. It's unclear to me why you need to append any data. What coordinates you use doesn't really matter because each run is independent from every other run (unless you see a specific need to take over a coordinate from an adjacent lambda). -- 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.