[gmx-users] Re: TI and heavy H

David Mobley dmobley at gmail.com
Wed May 17 19:07:11 CEST 2006


> 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.


> Best
> Luther
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