Yes, usually it would be a waste of time and energy to change the mass.
On Fri, Jun 20, 2008 at 10:17 PM, Qiang Li <[EMAIL PROTECTED]> wrote: > 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 > > > _______________________________________________ > 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
