[gmx-users] Simulation in different PH

[Justin A. Lemkul]

Sathish wrote:
> 
> Dear all,
> 
> How to run simulation in different PH?
> 
> Kindly help to fix this problem. Thanks in advance...
> 

The concept of "pH" is ill-defined for an MD system, the reasons for which have 
been discussed at length in recent days even (hint: please check the archive 
before posting).  Issues arise with the inability to change protonation, 
inadequate hydronium parameters, inability to model systems of sufficient size 
to even achieve a proper pH, and the list goes on.

The best you might hope for is not a change in "pH" (per strict definition), but 
rather changing the protonation state of titratable groups in your system 
according to pKa.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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