[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
>> chemical sense. The only problem I see is that if you have two atoms in
>> same location, while simultaneously turning one "on" and the other "off,"
>> will likely develop strong repulsive interactions between them such that
>> constraints may fail and your atoms will be displaced from the desired
>> 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
>> that sounds like a recipe for trouble.
> OK, thanks very much for the advice, however, I'm not following something
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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