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 <[EMAIL PROTECTED]> 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
[EMAIL PROTECTED]
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