What Mark means is that there us little meaning of adding ions in
a simulation of a protein in vacuum.
There is little sense and use of a simulation of a protein in vacuum,
but that could depend on what you are looking for.
There is little sense in putting ions in a vacuum environment to
neutralize your system, this does not depend on your problem.
The other option you have to neutralize the system is to neutralize
the side-chains so that here is no more net charges in your system.
This what is done in a Gromos FF version. check in the pdb2gmx options.
XAvier
I think, it is not a chemistry question exactly.
Genion command asks for a group whose atoms are replaced with ions.
I have no solvent molecules in my system.
In this respect, how can I incorporate ions into my system?
Check your assumptions. Does it make sense to put isolated ions outside a
protein in vacuum?
Mark
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XAvier Periole - PhD
1- Institute of Molecular Assemblies
City University of New York - USA
2- Molecular Dynamics-Group
University of Groningen - The Netherlands
http://md.chem.rug.nl/~periole
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