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.
