[gmx-users] How to choose the counter ions for proteins?
Mark.Abraham at anu.edu.au
Sat May 23 08:32:18 CEST 2009
Chih-Ying Lin wrote:
> How to choose the counter ions for proteins?
That depends what kind of system you're trying to model. Cellular
cytoplasm might have different ionic mixes from nerve synapses from agar
> Proteins are made of amino acids.
> Does it mean the counter ions of protein H+ or OH-?
It's instructive to calculate the ionic concentration of such ions at
biochemically relevant pH values and then to determine how many such
ions might be present in a typical MD simulation cell.
> I think => H+ and OH- ions are not available for the gromos force field, right?
> But, later version 4.0.2 ; they might be available, right?
That's what reading literature is for :-)
More information about the gromacs.org_gmx-users