Dear Gromacs users, I'm thinking about performing free energy calculations for a protein that binds cations, using alchemical transformation method. In the simplest case I'd transform an ion (one atom) into a naked particle; however in this case I'd get a non-zero overall charge of the system during the charge decoupling. I'm aware of some corrections for that and also that Gromacs probably neutralises the charge with PME (?). Another approach I've been thinking of is to simultaneously couple a naked particle somewhere in the bulk with the environment, switching on the charge in a same way as the charge of the ion is being switched off. In this way, the charge would be 0 all the time, and at the end of the simulation would yield the protein with an empty binding site and the ion somewhere in the bulk. Are there any obvious pitfalls with this approach?
Thank you, Wojciech -- 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.
