Thanks David, giving me some hints about what questions I might want to find answers for definetely sets me on the right track!
Cheers Luther >> I agree that there will be a d(Ekin)/dlambda term. It will actually >> occur >> independent of whether I shift mass from the oxygen to the dummy atom or >> not as the oxygen will not have the nitrogen's mass in any case. >> Still a dummy atom will affect phase space. I suppose I am not sure >> about >> how exactly it will do that (I don't think it is included in the >> evaluation of the potential and kinetic energy of a molecule). This is >> why >> I don't understand whether to transfer some mass to the dummy atom or >> not. >> Do you have a clue about the effects of a dummy atom on momentum space? > > So far, all of the free energy calculations I've done have involved > thermodynamic cycles where I disappear a ligand from a protein on one > side and from water on the other side, so all of these effects cancel > out. So I can't speak from experience. However, if I were doing > transformations which involved computing the free energy of changing > something with one number of atoms into something with a different > number of atoms, I'd be concerned about these issues. I don't have any > references, but I'm sure there's something in the literature on this. > Some particular concerns might be (a) do the bonded terms left over > for the dummy atom need to be corrected for? (b) Does the dummy atom > perturb phase space in some other way? I suspect once you're able to > answer these questions for the case where you don't have heavy > hydrogens and you aren't shifting mass around, it will become more > clear how you should handle your case. > > Sorry I can't be more helpful. > > David _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
