[gmx-users] functionalized surface: counter ions ? PME or RF.
David van der Spoel
spoel at xray.bmc.uu.se
Fri Aug 18 07:59:16 CEST 2006
Diego Enry wrote:
> Hello everyone,
> I would appreciate some advice on my simulation.
> The System is a Protein attached to a small Funcionalized 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 counterions ? Randomly ?
> 2) And what about long-range electrostatics ? PME would be fine, or
> should I try Reaction-Field ?
Add 250 Na+ and use PME. This corresponds to slightly less than
physiological salt concentration (which is roughly 1 NaCl per 330 water
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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