[gmx-users] Should I keep the total charge unchanged?

[Mikko Hellgren]

Hi Gromacs Users!

I am doing simulations on a small peptide and looking at the binding 
of zinc to cys. When I change the protonation of the cys (0 to -1), 
should I counterbalance this charge with one less Cl- atom to get a 
neutral system, and if so why? If I compare energies between different 
protonation states, how should I handle this change in the system 
(with a different amount of Cl-)? 

Many thanks in advance
Mikko Hellgren, Graduate Student at Karolinska Institutet in Sweden

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