Yes, Fig.6 comes from the different step in Fig.1. I think the easiest way here is to have 6 different "topol-mdp" files corresponding to each step. Although unlike the amino acid, defining the [ moleculetype ] for ion and a limited number of water molecules out of thousand of water molecules in the box would not be that easy.
The harmonic restrants have been applied in step 1 and 3, can you please let me know what is the difference between them and also how I can apply each of them in md files? Thanks, Regards, Alex On Tue, Jul 12, 2016 at 11:33 AM, Hannes Loeffler < hannes.loeff...@stfc.ac.uk> wrote: > 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. > -- 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.