[gmx-users] Dummy atoms for electrostatics calculation

Bob Johnson robertjo at physics.upenn.edu
Thu Mar 9 17:58:24 CET 2006

Hello everyone,
My system consists of a single stranded DNA adsorbed on a carbon nanotube. I
would like to calculate the electrostatic potential at the surface of the
nanotube due to DNA, water and counterions. Right now, each nanotube atom has a
charge of 0. What I would like to do is the following:

1) Assign a small identical charge (+0.001 say) to each nanotube atom

2) Run MD and calculate the Coulombic energy between the nanotube and the

3) The average potential that the nanotube sees is then this energy divided by
the total nanotube charge

The only problem with this is I do not want the nanotube charges to affect the
dynamics of the molecules in the environment. In other words, I want the DNA,
water, counterions to see an uncharged nanotube for the purpose of calculating
the trajectories. Is there any way to do this with dummy atoms?
Bob Johnson

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