[gmx-users] constant PH simulations

Gerrit Groenhof ggroenh at gwdg.de
Wed Sep 7 14:00:48 CEST 2011

> Message: 1
> Date: Wed, 07 Sep 2011 12:01:00 +0200
> From: "Emanuel Peter" <Emanuel.Peter at chemie.uni-regensburg.de>
> Subject: Antw: Re: Antw: Re: Re: [gmx-users] constant PH simulations
> To: <gmx-users at gromacs.org>
> Message-ID: <4E675CFC020000F100014EB3 at gwsmtp1.uni-regensburg.de>
> Content-Type: text/plain; charset="iso-8859-1"
> At first I would like to say that I deeply apologize for 
> the cave-like things I have said. I again say, that this
> was not the field I am deeply involved.
>> From Gerrit I got a banana.
> For this guy, I am a cave-man.

No, a monkey, just like you signed one of your earlier mails.

The questions you raise are all unaswered, but extremely relevant. Futher open discussion is highly appreciated.

> Generalized forces and averages for H+ interchange ?

The idea is that the protons are degrees of freedom. Protons can thus appear "spontaneously" on titrating sites. The driving force is the thermodynamic force: DG/Dl. More details can be foudn in the papers By Charly Brooks, JAna Khandogin and ourselves.

> Comparison with titration experiments ?

Not many of these around, but these will be crucial to establish the validty of the different approaches.

> Is there any experimental evidence for the rates of
> interchange ?

NMR maybe.

> Are simulation-times or the periods of interchange at 
> any time realistic?

Probably not.

> Are equilibria sampled well, with such interchanges,
> or are there jumps in free energy by this interchange ?

No the system follows the underlying free energy landscape always. THerefore there are no jumps, as one may habe in MC approaches. However, the price one pays is that one does sample intermediate state, in which the proton is only partially there.

> Why is there no free H+ ?

That would give an enormous sampling problem. Furthermore, the properties of MM hydroniom are very different from real hydronium

Hope this adds to the discussion.


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