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

David van der Spoel spoel at xray.bmc.uu.se
Tue Jan 30 08:50:00 CET 2007

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?

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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