Long-range force and moment calculations in multiresolution simulations of molecular systems

  • Authors:

  • Mohammad Poursina;Kurt S. Anderson

  • Affiliations:

  • Computational Dynamics Laboratory (CDL), Department of Mechanical, Aerospace and Nuclear Engineering, Rensselaer Polytechnic Institute (RPI), Troy, NY 12180, United States;Computational Dynamics Laboratory (CDL), Department of Mechanical, Aerospace and Nuclear Engineering, Rensselaer Polytechnic Institute (RPI), Troy, NY 12180, United States

  • Venue:
  • Journal of Computational Physics
  • Year:
  • 2012

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Abstract

Multiresolution simulations of molecular systems such as DNAs, RNAs, and proteins are implemented using models with different resolutions ranging from a fully atomistic model to coarse-grained molecules, or even to continuum level system descriptions. For such simulations, pairwise force calculation is a serious bottleneck which can impose a prohibitive amount of computational load on the simulation if not performed wisely. Herein, we approximate the resultant force due to long-range particle-body and body-body interactions applicable to multiresolution simulations. Since the resultant force does not necessarily act through the center of mass of the body, it creates a moment about the mass center. Although this potentially important torque is neglected in many coarse-grained models which only use particle dynamics to formulate the dynamics of the system, it should be calculated and used when coarse-grained simulations are performed in a multibody scheme. Herein, the approximation for this moment due to far-field particle-body and body-body interactions is also provided.