[gmx-users] Re: TI and heavy H

reich at mpikg.mpg.de reich at mpikg.mpg.de
Wed May 17 10:13:33 CEST 2006

> Date: Tue, 16 May 2006 09:29:36 -0700
> From: "David Mobley" <dmobley at gmail.com>
> Subject: Re: [gmx-users] TI and heavy H
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
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> 	<bc2c99750605160929l2a8fc8e3pf1d4640d5db1e3a3 at mail.gmail.com>
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> Luther,
>> I actually thought I would switch off an atom`s charge and LJ
>> interactions
>> if I transform it into a dummy atom. Is this wrong?
>> I am worried about the mass of the atom a heavy hydrogen is attached to.
>> In an amino group with heavy hydrogens the mass of the nitrogen is
>> decreased to about 8u since some of its mass is transferred to the
>> hydrogens. If I want to make a hydroxyl group of the amino group in
>> thermodynamic integration one of the hydrogens has to become a dummy
>> atom.
>> My question is whether I should decrease the mass of the oxygen as it is
>> connected to the heavy dummy atom. I wouldn't decrease its mass if the
>> dummy atom were derived from a normal hydrogen but what shall I do in
>> the
>> case of a heavy hydrogen? I am pretty sure that the decision will have
>> an
>> effect on momentum space and therefore the outcome of the thermodynamic
>> integration.
> I've never done anything with heavy hydrogens, but I think if you are
> going to turn an amino group into a hydroxyl group, you want to end up
> with a hydroxyl group that has the right mass, so this is something
> that is right to be concerned about. I can't say anything too
> definitive, but my advice is to make sure you end up with the right
> end states, even if it involves changing masses. I think normally if
> you involve some transformation which involves changing one atom type
> into another with a different mass, you WILL have a d(Ekin)/dlambda
> term which makes a contribution to the free energy of the
> transformation.
> David

Hi David,

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?



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