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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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