[gmx-users] pH studies

Justin A. Lemkul jalemkul at vt.edu
Sun Oct 11 17:48:28 CEST 2009

parthiban at ncbs.res.in wrote:
> Hi
> can any one could help me in, How to include the pH for doing MD studies.
> My interest is to include the pH at the initial time duration and to
> change the pH from 4 to 7 during the course of simulation.
> is there any possibility in performing such work in gromacs.

No.  Changing the pH over the course of a simulation would lead to changing the 
protonation state of titratable residues and is therefore not possible in MD, 
since you would be breaking and forming bonds.  Running independent simulations 
that represent different pH values might be more reasonable, by protonating 
these residues appropriately when running pdb2gmx and defining the topology that 
would correspond to a given pH value.


> Thanks in advance
> Parthiban
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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