Hello everyone,
I would appreciate some advice on my simulation.
The System is a Protein attached to a small Functionalized Surface
composed of ~250 positive carboxyl groups. The hole system is about
220,000 atoms. (amber,tip3p)
The big concern is how to deal with a net charge of almost "-250" ?
(guide me DNA guys)
1) Should I add a huge amount Na+ as counter ions ? Randomly ?
2) And what about long-range electrostatics ? PME would be fine, or
should I try Reaction-Field ?
Thanks,
--
Diego Enry B. Gomes
@ Pacific Northwest National Laboratory.
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.
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