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.
2) is it
possible to introduce any kind of "free radicals" to a system consisting
protein and solvent? i am trying to introduce some OH- radicals into my
protein (which is related to aging phenomena) and seek every kind of
stractural changes that occurred on the protein structure after some ns
whithout any covalent bond breaking or formation as the first events in
every chemical reactions! how can i do that?
... by waiting about fifty years. To actually model bond breaking such
as these radicals would be doing, you need to treat the electronic
degrees of freedom, and reliable ab initio molecular dynamics on whole
proteins will not be feasible for at least this long.
It does sound like you need to do some background reading on molecular
simulations and their capabilities and limitations.
Mark
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