[gmx-users] TI and heavy H

Mark Abraham Mark.Abraham at anu.edu.au
Tue May 16 16:32:48 CEST 2006

reich at mpikg.mpg.de wrote:
> Hi Lars,
> 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 would determine the underlying model of mass transfer used in the 
nitrogen case, like 2amu transferred from N to each H, and apply the 
same model to the oxygen case. I don't know whether there is a need to 
conserve mass over TI - consult the detail in the appropriate papers 
unless someone comes up with a comment.


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