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

[Emanuel Peter]

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.

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> 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> 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





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-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613


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