[gmx-users] pi stacking

soumadwip ghosh soumadwipghosh at gmail.com
Wed Apr 15 16:28:07 CEST 2015

Dear Tushar,
                    I dint get what you mean by 'effect of salt
concentration can not be simulated in GROMACS'. I am simulating a single
stranded DNA which is negatively charged in its native state and the added
salt is bound to affect its dynamics. This is of course valid if the force
field parameters chosen for the ionic species are correct and the dynamics
is studied for sufficiently long time in the realm of what we want to
study. There are numerous examples of protein as well as DNA dynamics
studied at different salt concentrations using MD.

Dear Justin,
                   So I guess when I am seeing two base pairs getting
stacked for a significant duration of time the interaction can be termed as
'stacking' whose interaction energies can be calculated by summing up the
short range non-bonding electrostatic and VDW energy terms. It appears to
me that this stacking is not a full pi-pi stacking since classical force
fields can not treat pi electrons or their polarizability explicitly.

Can you suggest me in short what am I supposed to reply to the reviewer's
query "'what the pi-stacking interactions actually correspond to (in the
real world) and how well these are captured in the empirical force field
description?" Should I cite some of the papers (like that of Chen & Garcia)
to show that Charmm deals reasonably well with non-bonded stacking
interactions? Can you suggest some more appropriate references? Or any
other comment regarding the reply of the above review. Thanks for your help
as always in advance.

Soumadwip Ghosh
Research Fellow

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