But even though on the other hand that could be more realistic free energy which could be compare to experiment which also involves ions. Would Justin please comment on this?
On Wed, Jul 31, 2013 at 11:46 AM, Steven Neumann <s.neuman...@gmail.com>wrote: > 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
