[gmx-users] Re: Reg: GROMACS Queries

[Justin A. Lemkul]

Please keep all GROMACS-related correspondence on the gmx-users list.  I do not 
advertise myself as a private tutor, nor do I claim to have all the answers. 
You stand a much better chance of getting useful information by posting to the list.

The concept of pH in a simulation is a difficult one.  You may find the 
information here useful:

http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation

In one sense, you can protonate residues according to how they would 
predominantly exist at a given pH, but you can't really account for the effects 
of proton transfer between residues.  Protonation states can be assigned when 
running pdb2gmx.

-Justin

Suguna wrote:
> Dear Justin,
> 
>  
> 
> Iam S.Sugunadevi doing my Ph.D. in Korea. Iam very new to this field 
> (Molecular Dynamics). I got your ID from GROMACS mailing list.
> 
>  
> 
> I would like to do MD in different pH values. Kindly, could you guide 
> me, where to include that pH values and how?
> 
>  
> 
> Iam eagerly waiting for your responds.
> 
>  
> 
> Kindly help me.
> 
>  
> 
> Thanks in advance.
> 
>  
> 
> Regards
> 
> Sugunadevi.S
> 

-- 
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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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