[gmx-users] Pi stacking potential and parameters in Gromacs?

Delmotte, Antoine antoine.delmotte09 at imperial.ac.uk
Tue Aug 21 11:17:14 CEST 2012

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 

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,


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