Hello,
I am going to run MD simulations (by AMBER 7) of a small protein
containing 8 non-compensated charged amino acid residues. I ‘d like to
carry out these simulations within the physiological electrolyte
concentrations 0.15 Mol/L. I need to have good accuracy to take into
account the short- and long- range electrostatic interactions.
#1. As I know, for application of the PME methods a neutral system is
required (Darden T, York D. Pedersen L. J. Chem. Phys., 1993.
98:10089-10092).
How to satisfy (by LEaP) both requirements to neutralize the system and
at the same time to create given electrolyte concentration 0.15 M?
#2. Could you recommend me how to right estimate number of counterions,
for example, Na+ and Cl- for given concentration 0.15 Mol/L?
Thanks for your consideration.
Sincerely yours,
UNMC Eppley Cancer Center
Molecular Modeling Core Facility
E-mail: arubin.unmc.edu
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Received on Fri Nov 19 2004 - 21:53:00 PST
