[gmx-users] Pi stacking

soumadwip ghosh soumadwipghosh at gmail.com
Wed Apr 15 08:03:06 CEST 2015

Hi all,
        I want to ask a very general question which was asked by one of the
reviewer of my paper. I have shown the stacking between different base
pairs of a single stranded DNA at different salt concentration. The
corresponding distances between the stacked base pairs were estimated using
g_dist and the energy terms were calculated using the g_energy and
selecting the coul:SR and LJ:SR parameters together between two stacked
residues which were specified as energy groups in the md.mdp file prior to
the final mdrun. What he has asked me is 'what the pi-stacking interactions
actually correspond to (in the real world) and how well these are captured
in the empirical force field description.' I know the pi-stacking in
principle is a sum of non-bonded electrostatic, dispersive , induced and
exchange term, basically a sum of non-bonded Coulomb and VDW terms within a
specified cut-off. How well these terms are captured in the force field
(CHARMM 27 which I used) is something I dont know. Do I have to cite some
references to show that others have calculated pi-stacking in a similar
manner or something more relevant to the CHARMM27 force field?

I am stuck with this query..Any kind of help would be greatly appreciated.

Thanks and regards,
Soumadwip Ghosh
Research Fellow,
IIT, Mumbai

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