[gmx-users] Re: BAR calculations with tabulated non-bonded potentials

Justin A. Lemkul jalemkul at vt.edu
Mon May 21 19:45:21 CEST 2012

On 5/20/12 2:30 AM, jrustad wrote:
> Justin A. Lemkul wrote
>> You don't need the pull code if the two atoms are in the same
>> [moleculetype] - a
>> "molecule" in Gromacs is any set of atoms; they don't necessarily have to
>> make
>> chemical sense.  The only problem I see is that if you have two atoms in
>> the
>> same location, while simultaneously turning one "on" and the other "off,"
>> you
>> will likely develop strong repulsive interactions between them such that
>> the
>> constraints may fail and your atoms will be displaced from the desired
>> location.
>>    I can't say for sure whether it will be a problem, but if you've got
>> atom A
>> existing at 20% and atom B trying to exist at 80% in the exact same
>> location,
>> that sounds like a recipe for trouble.
> OK, thanks very much  for the advice, however, I'm not following something
> here-
> maybe I am just being dense:
> I thought the point was that the Fe2+ and Fe3+ ions cannot be in the same
> molecule, because the lookup tables for their short ranged interactions need
> to be assigned using energygrps, which seem to apply to molecules not atom
> types.  If the tables could be applied to atom types rather than molecules
> (which makes more sense to me anyway), then there would be no problems.

You can assign energygrps to any valid group, though I honestly have no 
experience using such groups with tables.  It may work differently.

> I thought it was possible in GMX to completely switch off all interactions
> (including coulomb and vdw) between selected molecules.  If so, then when
> one "turns on" while the other "turns off" they never interact, correct?
> Maybe I am wrong that it is possible to exclude all interactions between two
> given molecules?

Forgive me, the enegrygrp_excl option slipped my mind when I wrote that last 
message, so yes, it should be possible to exclude their interactions.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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