[gmx-users] TI and heavy H

reich at mpikg.mpg.de reich at mpikg.mpg.de
Tue May 16 16:15:23 CEST 2006

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



> 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.
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