This is a tough issue and there are some unresolved questions here. I recommend seeing the work of Kastenholz and Hunenberger on ion solvation in JCP a couple years ago (two companion papers) as these explain the key issues.
Thanks. On Wed, Aug 17, 2011 at 3:24 AM, Marcelino Arciniega Castro < macas...@mytum.de> wrote: > Hi there, > > Could someone please share some ideas about the next situation?: > > I am trying to estimate the relative binding affinity of two small > molecules to a protein. In the setup process, ions are added in the solvent > to neutralize the system. Then as everybody suggest, the ligand partial > charges should be decouple to zero. But my specific case, the small > molecules are charged, that means that after turning off the ligand partial > charges, the system will have a net charge (because the ions in the > solvent). Turning off the ions charges does not solve the problem, because > of the protein charges. > > The concrete question are: > Should I continue to atom mutation step using PME in a non-neutral system? > It would make sense to turn off the partial charges of the some atoms in > the small molecule (just those that are going to be mutated)? > > Thanks in advance > Marcelino > -- > 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 > -- David Mobley dmob...@gmail.com 504-383-3662
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