[gmx-users] functionalized surface: counter ions ? PME or RF

Gomes, Diego Enry B diegoenry.gomes at pnl.gov
Fri Aug 18 07:16:46 CEST 2006

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 ?

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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