[gmx-users] MD simulation with varying pH

Gaurav Goel gauravgoeluta at gmail.com
Thu Jul 5 09:29:17 CEST 2012

Dear Peterson,

There's no magic wand for this. You'll need to find out pKa values of
titrable amino acids in your protein (in literature, MEAD software,
etc.). Then, you can protonate (pH<pKa) / deprotonate (pH>pKa)  those
group according to the pH.


On Thu, Jul 5, 2012 at 12:33 PM, J Peterson <think_beyond at aol.com> wrote:
> Dear GROMACS Users,
> I'm planning to work on a protein that activates itself under lower pH
> conditions. And I don't have any clues how to do it in GROMACS. My first
> question is about the possibilities to do this in GROMACS, has anyone done
> this before? It can even be a constant simulations at a particular
> lower/higher pH or gradually lowering/increasing pH.
> Any suggestion on this would give me a lead.
> Thanks
> Peterson J
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Gaurav Goel, PhD
Assistant Professor
Department of Chemical Engineering
Indian Institute of Technology, Delhi
Hauz Khas, New Delhi 110016

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