[gmx-users] pH studies

Miguel Machuqueiro machuque at fc.ul.pt
Sun Oct 11 20:14:46 CEST 2009

On 11-10-2009 16:48, Justin A. Lemkul wrote:
> 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.
> -Justin

Hi there,

Just to mention that a pdb2gmx topology only reflects one pure 
protonation state of your system (protein) and even if at a given pH 
that is the most abundant state, one should not generalize. Classical MD 
does not deal with pH even if sometimes people claim that it does.

To deal with pH in MD one should have a look at Constant pH MD methods:


You can have a look at this paper to have an idea on which methods are 
being developed these days.

Machuqueiro, M., Baptista, A.M. (2006), J. Phys. Chem. B, 110, 
2927-2933. http://dx.doi.org/10.1021/jp056456q



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