They do not dissociate...Are you sure? My mdp specifies only ligand as a pull_group1. I think it would change having ions in this group included.
On Wed, Jul 31, 2013 at 11:01 AM, lloyd riggs <lloyd.ri...@gmx.ch> wrote: > > >will get the PMF profile for my > >ligand binding or ligand and two ions binding? > > It would be the ligand and two ions unless the ions also at some point > discossiate from the ligand once in solvent. Could add positional restraint > for them, but dont know how that effects the calculation? > *Gesendet:* Mittwoch, 31. Juli 2013 um 09:29 Uhr > *Von:* "Steven Neumann" <s.neuman...@gmail.com> > *An:* "Discussion list for GROMACS users" <gmx-users@gromacs.org> > *Betreff:* [gmx-users] Umbrella Sampling > Dear Gmx Users, > > I run SMD to extract the windows for US calculations. The system involves > negatively charged ligand and protein. I generated the protein-ligand > complex within self assembly MD simulations. > > I pulled my molecule away and two ions were also detached from the protein > surface being attached to my ligand. > > My question: if I run my US caluclation and combine windows by WHAM (I > specified in my umbrella.mdp my ligand as a pull_group1 and same protein > residues I pulled it from as pull_group0) will get the PMF profile for my > ligand binding or ligand and two ions binding? > > Steven > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
