[gmx-users] Re: gromacs and pH description!

Jay Mashl mashl at uiuc.edu
Tue Jan 30 15:16:31 CET 2007

On Tue, 30 Jan 2007, David van der Spoel wrote:
> Mark Abraham wrote:
>>  Florian Haberl wrote:
>> > >  1) how can i explaine "pH" into my system ( consisting protein & Na+ 
>> > >  ions
>> > > )  under gromacs? i'd like to reach to pH ~ 4.5 or 5 in my system.
>>  What concentration of H+ ions are needed to get to these pH values? Can
>>  you do that in a system with 10^4 to 10^5 atoms? Even if you can, there
>>  are no MD water models that allow hydrogen atoms to dissociate freely, as
>>  happens in real water.
> This is not entirely correct, there are constant pH simulation models, 
> developed by Charlie Brooks and others where you can simulate transfer of 
> protons from one side chain to another. THis is not exactly what you need 
> here, and they only work in implicit solvent so far (and in Charmm at that). 
> I'd like to have such models implemented in gromacs, and with explicit 
> solvent. Anyone interested?

I think there is a general need for it. After having just finished some work on 
protonation states without the benefit of an implementation built into Gromacs, 
I have been thinking about how to do just that.


R. Jay Mashl
University of Illinois
mashl at uiuc.edu

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