Syma Khalid wrote:
Dear all,
I was wondering if someone could offer some advice?
I would like to run an atomistic langevin dynamics simulation (as I
don't want to include water explicitly). If I add the appropriate
langevin dynamics options in the mdp file, then is there any reason why
I shouldn't use explicit counter ions (unfortunately my protein has an
overall charge)?
In what medium are they going to move? How realistic is that going to be?
Obviously I would use periodic boundary conditions so the ions don't
wander off.
If they really are just counter-ions, then simple electrostatics will do
that... this is a side-issue, however.
Mark
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