AMBER Archive (2004)

Subject: AMBER: Electrolyte concentrations in MD

From: arubin_at_unmc.edu
Date: Fri Nov 19 2004 - 14:56:09 CST

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_at_unmc.edu
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