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

[Justin Lemkul]

On 8/21/12 5:17 AM, Delmotte, Antoine wrote:
> 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?
>

The force fields in Gromacs do not include an explicit pi stacking term.

> 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...
>

To calculate an energy, one needs a topology (that requires pdb2gmx) and some 
representation of an environment (solvent) which means genbox or implicit 
solvent settings in grompp, which is the precursor to mdrun, which calculates 
the values inherent to a simulation (forces and energies).  One can easily do a 
single-point energy calculation, but there is no way to do this simply from a 
.pdb file.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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