Looking into the manual, i find under the 'energy monitor group':
'Mutual interactions between all energy monitor groups are compiled
during the simulation. This is done separately for Lennard-Jones and
Coulomb terms. In principle up to 256 groups could be defined, but that
would lead to 256x256 items! Better use this concept sparingly. All
non-bonded interactions between pairs of energy monitor groups can be
excluded (see sec. 7.3). Pairs of particles from excluded pairs of
energy monitor groups are not put into the pair list. This can result in
a significant speedup for simulations where interactions within
or between parts of the system are not required.'
But i found nowhere an option to tell GROMACS to handle the exclusions
for LJ and Coulomb interactions differently. Don't know if it's
possible. For standard exclusions it seems that LJ and Coulomb
interaction get treated equally -> if one excludes one, one also
excludes the other...
One idea: But only possible if one can define two bonds, between the
same atoms. I don't know if this is possible.
One idea for a work-around would be the following (but it will slow the
simulation). Exclude all 1-2 and 1-3 interactions. To get the Coulomb
interacions back, construct table interactions for bonds.
GMX manual 4.5.3:
Look for '4.2.13 Tabulated interaction functions' and '6.7 Tabulated
interaction functions'
It seems that one can construct tabulated interactions also for bonds.
Potential looks like:
V = k * f(r)
where f(r) is a cubic spline, think here one could use the values for
the coulomb-interaction for the non-bonded table.
For k use the product of the two charges. In the topology, one would
need to write both atoms and this force-constant (our product of
charges), similar to normal bonds.
If two bonds between the same atoms are not possible, one could define
tabulated interactions for the bonds + Coulomb interactions ... but this
would be a lot of work. Probably it would be easier, to hack GMX, that
it ignores Exclusions for Coulomb interactions.
Or another persons has hopefully a better idea.
Greetings
Thomas
Hi all,
I am attempting to simulate a system that has strong ionic character so I would
like to treat the electrostatics and van der Waals interactions separately.
For example I would like to include all pairs of atoms in the electrostatics
calculation but I would like to exclude 1-2 and 1-3 neighbors in the van der
Waals calculation. Is this possible to do in GROMACS? If so, how might this
be accomplished? Thanks in advance for your help.
Jeff Woodford
Assistant Professor of Chemistry
Missouri Western State University
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