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 ?
Thanks,
Add 250 Na+ and use PME. This corresponds to slightly less than
physiological salt concentration (which is roughly 1 NaCl per 330 water
molecules).
--
David.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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