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

jrustad rustadjr at corning.com
Sun May 20 02:30:56 CEST 2012

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
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.

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?

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