[gmx-users] Using lennard jones and buckingham terms simultaneously
matthew.watkins at ucl.ac.uk
Tue Mar 23 16:39:15 CET 2010
as Vitaly suggested tabulated potentials seem to be the only way to go,
it took me a while to get up to speed on the Gromacs way of doing this,
so get in touch if you wish.
The tables for buck potentials need to include the standard 1/r6 term
whilst what would be the 1/r12 term needs to contain exp(-Bx.rho), the
C6 and C12 coefficients can then be put in a standard nonbonded section.
You'll need a separated table for each pair of interactions that
interact with buckingham potential. Each pair must be an energy group
If there is a simpler method I'd love to hear it.
Gareth Tribello wrote:
> I would like to use gromacs-4 to do a simulation of a small protein in
> water and in the presence of calcium carbonate. The potential I have
> for the calcium carbonate uses Buckingham terms for the interaction
> between the calcium and carbonate ions, while the protein obviously
> interacts through Lennard Jones terms. It is my understanding from the
> manual that it is not possible to mix these two interaction types and so
> it is not possible to do this simulation. Also when I attempted to mix
> lennard jones and buckingham terms in a topol.top file grompp complained.
> Is there anyway around this problem?
> Many thanks
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