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

[David Mobley]

I agree that this would be a good idea. We would need to think
carefully about how to validate it though.



On 1/30/07, Jay Mashl <mashl at uiuc.edu> wrote:
> 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.
>
> Jay
>
> --
> R. Jay Mashl
> University of Illinois
> mashl at uiuc.edu
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