Hi Qiang, Couldn't you do it by shortening the chain, turning on/off one of the CH2 groups? You only have to mind perturbing the bonding and such in the right way then.
Cheers, Tsjerk On Sat, Sep 27, 2008 at 6:32 PM, 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 > Mobley's suggetion, 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? > > thanks 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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
