Concerning to the harmonic restraints, in step 1. is just something inside the molecule (as said applying restraints to the H and O atoms in HCOO-) but in step 3 is restraint between waters molecules and surface, but my question is in general how I should apply the harmonic restraint? If it is by the "restraint-lambdas"? should I use "posre.itp"? should I use pull code?
Thanks Regards, Alex On Tue, Jul 12, 2016 at 2:40 PM, Hannes Loeffler <hannes.loeff...@stfc.ac.uk > wrote: > On Tue, 12 Jul 2016 12:44:10 +0200 > Alexander Alexander <alexanderwie...@gmail.com> wrote: > > > 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. > > I think it should be fairly straightforward to define two new > moleculetyps with a new name each, rename and reorder the coordinate > file accordingly and make the few changes in the [molecules] section. > > > > 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? > > You would need to read the paper. Since this is a decoupling exercise > my guess would be that the restraints are relative to the Ti surface. > -- > 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.