[gmx-users] TI and heavy H

David Mobley dmobley at gmail.com
Tue May 16 18:29:36 CEST 2006


> 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


> Best
> Luther
> > Message: 1
> > Date: Tue, 16 May 2006 09:53:27 +0200
> > From: Lars Schaefer <Lars.Schaefer at mpi-bpc.mpg.de>
> > Subject: Re: [gmx-users] TI and heavy H
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <446984F7.70107 at mpi-bpc.mpg.de>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Hi Luther,
> > why do you want to switch the charges of your  heavy H's off? You could
> > just switch the charges and LJ  interactions off, and leave the masses
> > as they are.
> > Best,
> > Lars
> >
> > reich at mpikg.mpg.de wrote:
> >
> >>Dear Gromacs users,
> >>
> >>I want to perform a thermodynamic integration using heavy H´s in my
> >>system. I am somewhat confused  about how to deal with dummy atoms that
> >>originate from heavy H´s. Do I still have to substract the appropriate
> >>mass from the atom the dummy atom is attached to? I suppose I would
> >> change
> >>the momentum part of phase space otherwise.
> >>
> >>Cheers
> >>
> >>Luther
> >>
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