Antw: Re: [gmx-users] constant PH simulations

[Justin A. Lemkul]

Emanuel Peter wrote:
> Could you just tell me smth. !
> No forcefield on whole earth is able to reproduce the pH realistically
> by H+.
> You just can apply pH of your system through the protonation states
> of each part in your system.
> 

Constant protonation state and constant pH are different.  Gromacs does not have 
the capability of doing constant pH simulations since such algorithms (i.e. 
http://mmtsb.org/workshops/mmtsb-ctbp_workshop_2009/Tutorials/CPHMD/cphmd_tutorial.html) 
are not implemented.  One can make an argument that comparing protonation states 
can be useful (I've done it), but you cannot equate constant protonation with 
constant pH.

-Justin

> monkey.
> 
> 
> 
>  >>> João M. Damas 06.09.11 14.22 Uhr >>>
> That is not considered constant-pH MD.
> 
> Follow Justin's suggestion.
> 
> Cheers,
> João
> 
> On Tue, Sep 6, 2011 at 12:47 PM, Emanuel Peter 
> <Emanuel.Peter at chemie.uni-regensburg.de 
> <mailto:Emanuel.Peter at chemie.uni-regensburg.de>> wrote:
> 
> 
>     Look for the pKa-constants of each part of your system (e.g. each
>     amino-acid).
>     Then you can check each protonation state and change it according to
>     your
>     application in the force-field.
> 
>     Emanuel
> 
>      >>> fancy2012 __ 06.09.11 13.01 Uhr >>>
>       Dear gmx users,
> 
>     Are there some tutorials on constant PH simulations using gromacs?
>     How should I state my work? Right now I have no idea on it.
> 
>     --
> 
>     _Best wishes,_
> 
>     _Qinghua Liao_
> 
>     _Ph.D student of Tianjin University, China_
> 
>     __
> 
>     --
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> 
> 
> 
> -- 
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
> 

-- 
========================================

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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