[gmx-users] Charge neutralization

Arden Perkins perkina2 at eou.edu
Thu Dec 10 07:33:47 CET 2009

Hey all, I am trying to examine couplings between Mg+2 ions and a peptide
with a -5 charge. I would like to optimize couplings and have considered
using a +1 charge from the system. I read that GROMACS can do this and that
in theory it should have the same effect as adding ions but it is not
standard practice. For future simulations I plan to increase the [Mg+2] and
am worried about couplings from Cl- if I were to use Cl- to neutralize the
excess positive charge. Is it ok to use the system to neutralize these
charges? Or is that considered a bad experimental design?

Thanks for you feedback!

Arden Perkins
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