[gmx-users] pH

Miguel Machuqueiro machuque at itqb.unl.pt
Sun May 20 22:33:52 CEST 2007

> 20 maj 2007 kl. 20.59 skrev David van der Spoel:
>> Dmitriy Golubovsky wrote:
>>> Dear Guru!
>>> have you got any idea, on what how to calculate pH. for the system?
>>> i'm solving a promblem of coil-globule transition for polymer.
>>> do the topology for my structure(opls ff), do MD in water (spc).
>>> get the statiscts. everything is ok.
>>> the summary charge is equal to zero. no dissociation.
>>> so the question is - how to calculate pH. or it's not possible?
>>> if it is possible, than how to variate this pH in some range.
>>> I allready try to use genion, but didn't get good results, on case
>>> of very big dependence of the results from the initial
>>> conformations of ions.
>> How about computing the H3O+ concentration?
>> It is close to impossible to simulate realistic pH with limited
>> size systems. In practice your pH is always seven.
> Depending on your specific application, CPHMD can be used to simulate
> with constant pH. Unfortunately, CPHMD utilizes lambda-dynamics,
> which is not yet implemented in gromacs. It should not be THAT hard
> to implement yourself if you know a thing or two about MD and
> programing in general.

If you are interested in Constant-pH methods, you can take a look at:

Machuqueiro, M., Baptista, A.M. (2006) “Constant-pH Molecular Dynamics
with ionic strength effects: The protonation–conformation coupling in
decalysine”, J. Phys. Chem. B, 110, 2927-2933.

and several references therein.

And... as a reminder, our method is implemented with Gromacs.

Miguel Machuqueiro
ITQB-Instituto de Tecnologia Química e Biológica
Universidade Nova de Lisboa
Molecular Simulation Group - 6º Floor
Av. da República, EAN, Apartado 127
2781-901 Oeiras, Portugal

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