Dear Gromacs users,
I am currently trying to get an expression of the energy of pi stacking
interactions (in DNA) and I would like to know how it is calculated in
Gromacs.
I guess that Gromacs is estimating the energy of the pi stacking as the
sum of the van Der Waals and electrostatics contributions using
quardrupoles. Is that correct or am I missing something?
Secondly, would anyone know where I could find the exact expression and
the values parameters used?
I imagine that I would need in particular:
- The parameters of the van Der Waals term
- The charges associated with each atom
- The position of the charges of the quadrupole relative to the
nucleus of the atom
I have no preference in the force field used really, as long as it can
give me a reasonable value of the pi stacking interaction. The
calculations I am doing are for DNA, and I would like to calculate the
energy of the pi stacking interactions from the pdb file directly, and
without having to run Gromacs...
Any help on this issue will be greatly appreciated!
Many thanks in advance,
Antoine
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