[gmx-users] Treating electrostatics and van der Waals interactions differently

[Thomas Schlesier]

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