AMBER Archive (2004)

Subject: AMBER: Electrolyte concentrations in MD

Date: Fri Nov 19 2004 - 14:56:09 CST


  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.
  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
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