Hi, As long as you end up with the same charge in the initial and final states, you should be OK. It's only if your total transformation involves a change of net charge that you need to worry. So you should be fine if you turn off the charges on D, change the LJ interactions, and turn back on the charges on E.
If I were you, I probably would not turn off the charges entirely -- after all, D and E share many atoms. I would only turn off charges on the atoms that you are going to modify. David On Fri, Sep 26, 2008 at 2:14 AM, friendli <[EMAIL PROTECTED]> wrote: > Dear all, > > I have a mutation free energy calculation from D(asp) to E(glu). The charge > is not changed for the overall mutation. However, following Dr. David > Molbey's suggesion, electrostatic and VDW interaction should be modified > separately, so in the first step we need to turn off the charge from D(-1) > to D(0). > > I learn from the mailing list that it is problematic to do FE calculations > with different charges for initial and final states. > So is that safe to turn off the charge for D and turn on the same charge for > E in this case? > If not, it that OK to perform mutation FE calculation in one step? > or there is no safe way to handle this kind mutations, i.e. mutating charge > groups, currently without special correction? > > thank a lot > > Qiang > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
