[gmx-users] Changing the pH

[João Henriques]

Hi Tanos,

Perhaps you should try one of the available constant-pH MD methods. Here is
a quick explanation of what they do and who is involved in their development
right now:

http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation
My opinion regarding this subject may be a little biased since I've worked
with one of the most active researchers in this area, but I would suggest
you to read some papers from Antonio Baptista and/or Miguel Machuqueiro
(from Baptista's 2002 initial "Constant-pH molecular dynamics using
stochastic titration" paper to nowadays).

Best regards,

On Tue, May 10, 2011 at 7:22 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Tanos Celmar Costa Franca wrote:
>
>>
>> Dear GROMACS users,
>> Does someone now how to procede to change the pH of a MD simulation from
>> the physiologic one (7.4) to 6.5 ?
>>
>>
> Classical MD simulations do not currently allow for dynamic proton
> exchange. The best you can do at the moment is use pdb2gmx to set the
> protonation state of titratable residues.  At pH 6.5, histidines will be
> quite annoying to deal with properly.
>
> -Justin
>
>
>
>> Tanos Celmar Costa Franca - D.Sc
>> Coordenador do Programa de Pos-graduacão em Química
>> Secão de Engenharia Química - SE/5
>> Instituto Militar de Engenharia - IME
>> Rio de Janeiro - RJ
>> Brasil
>>
>>
>>
>>
>>
>> ----------------------------------------------------------------
>> This message was sent using IMP, the Internet Messaging Program.
>>
>>
> --
> ========================================
>
> 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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-- 
João Henriques, MSc in Biochemistry
Faculty of Science of the University of Lisbon
Department of Chemistry and Biochemistry
C8 Building, Room 8.5.47
Campo Grande, 1749-016 Lisbon, Portugal
E-mail: joao.henriques.32353 at gmail.com / jmhenriques at fc.ul.pt
http://intheochem.fc.ul.pt/members/joaoh.html
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