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How Can I simulate macroions for electrophoretic flow using molecular dynamics simula

  1. Apr 25, 2012 #1
    Hi dear all
    I am working on electrophoretic flow and I want to simulate macroions which are large complex molecules consisting charged atoms. As I know we can consider that a macroion is a large sphere (or cylindrical) particle with a hydrodynamic radius with the net charge of forming atoms.
    But there is a question and that is how can I specify the gender of macroion. I am using lennard-jones potential which needs σ and ε coefficients and I dont know how to obtain them.
    In papers that I read they specify the diameter, mass, charge, and lennard jones coefficients of an sphere macroion without saying anything about what is this macroion and it consist how many particles and what is its gender. also they show the effect of varying σ and ε on results. So what is your idea for me to simulate true macroions. Do you think this is better to simulate polymers or no I can consider sphere particles? And if I can, How can I obtain its characteristics?
    please give me suggestions with refrences.
    Thanks alot
    Best regard
    Majid
     
  2. jcsd
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