Hi Gareth,
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
as well.
If there is a simpler method I'd love to hear it.
Cheers,
Matt
Gareth Tribello wrote:
Hello
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
Gareth
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