You can change the mass if you like. Basically, the net free energy change associated with changing the mass should end up being zero so it will be irrelevant. The mass of course affects the dynamics and things like the velocities, but based on equipartition you can convince yourself that the free energy change will be zero.
David On Fri, Jun 13, 2008 at 12:04 AM, friendli <[EMAIL PROTECTED]> wrote: > Dear all, > > I am calculating FE using TI. I have a question about mutating existing > atoms with different mass. > for example, using ffG53a6 force field, in one case i need to mutate CH2 to > CH3, > should I use > [ atoms ] > 17 CH3 2 ALA CB 6 0 15.035 CH2 0 > 14.027; qtot 1 > > OR > > 17 CH3 2 ALA CB 6 0 15.035 CH2 0 > 15.035; qtot 1 > > I notice from Prof. Alan Mark's online FE course, he mutates a H atom to a O > atom, but does not change its mass. > The line is : > 12 HC 1 PHE HZ 6 0.1 1.008 > OA -0.548 1 1.008 > > Can somebody explain a bit why we should not change the mass accordingly? > > > thank you > > LQ > > I though I sent this email but why I can not see it. There may be something > wrong with my email software. so I send here again. sorry > _______________________________________________ > 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
