[EMAIL PROTECTED] 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.
Mark
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