Thanks for clearing the doubt. Is that more easier to get equlibrium to use unchanged mass when doing LJ turning on/off? I ask this since I found the forwards and backwards mutation free energy are more consistant if I do not change the mass. Accidentally?
LQ On Thu, Jun 19, 2008 at 4:26 AM, David Mobley <[EMAIL PROTECTED]> wrote: > 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 >
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