Re: DNA system and PH control

From: Aron Broom (
Date: Mon Mar 19 2012 - 12:54:11 CDT

Do you mean that you want to run several different simulations, each at a
discrete pH?

I don't think NAMD allows for constant pH simulations, but maybe this has

You could try some kind of poisson-boltzman solver in order to estimate the
pKas of your groups, which will depend properly on their environment and
not just some general pKa. Without constant pH simulations, however,
you'll just be stuck in each simulation with a particular group being in a
particular ionization state, which will be inaccurate for any groups whose
pKa is near the pH you are simulating.

Overall pH in a simulation is a pretty tricky thing.


On Mon, Mar 19, 2012 at 1:42 PM, raghav singh <>wrote:

> Hello All,
> I just wanted to how can I control/ describe variable PH using VMD/NAMD
> for a DNA based system.
> I want to run simulation for different PH scales.
> Thank You
> regards
> Raghav

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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