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
Best Luther _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
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