[gmx-users] constant PH simulations

[João M. Damas]

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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