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

[Justin A. Lemkul]

Emanuel Peter wrote:
> The standard procedure of H+ interchange and transition states can be done
> through QM/MM.
> Please give one reference according to the algorithms you have mentioned.
> 

There are several cited at:

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

-Justin

> Cheers.
> 
>  >>> João M. Damas 06.09.11 15.19 Uhr >>>
> As Justin said, constant protonation != constant pH.
> 
> Constant-pH MD does not simulate H+, but allows changes in protonation 
> states during the MD simulation. There are different algorithms 
> to accomplish that.
> 
> Cheers,
> João
> 
> On Tue, Sep 6, 2011 at 2:04 PM, Emanuel Peter 
> <Emanuel.Peter at chemie.uni-regensburg.de 
> <mailto:Emanuel.Peter at chemie.uni-regensburg.de>> 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.
> 
>     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 <tel:%2B351-214469613>
>     __
> 
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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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