Hi I want to calculate the change in free energy (electrostatic contribution only) when introducing a charge in a certain site of a protein using a single step FEP.
Should this be done with charging an inserted virtual site (a dummy atom) or a protein atom (e.g. Ca)? I noticed that in the case of the dummy atom, the Coul-14:Protein-vsite zero. I am not sure why though... Thanks a lot in advance for any feedback. Best wishes George Dr. George Patargias Polymer IRC Group University of Leeds Leeds, LS2 9JT, UK _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
