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

Mohammad Poursina, Kurt S. Anderson

Research output: Contribution to journalArticle

12 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)7237-7254
Number of pages18
JournalJournal of Computational Physics
Volume231
Issue number21
DOIs
StatePublished - Aug 30 2012
Externally publishedYes

Fingerprint

moments
simulation
RNA
DNA
Torque
Proteins
Molecules
center of mass
far fields
torque
deoxyribonucleic acid
interactions
continuums
proteins
approximation
molecules

Keywords

  • Biopolymers
  • Coarse-grained molecular systems
  • Long-range interactions
  • Multiresolution problems
  • Pairwise interactions
  • Pseudo-center
  • Pseudo-inertia tensor

ASJC Scopus subject areas

  • Computer Science Applications
  • Physics and Astronomy (miscellaneous)

Cite this

Long-range force and moment calculations in multiresolution simulations of molecular systems. / Poursina, Mohammad; Anderson, Kurt S.

In: Journal of Computational Physics, Vol. 231, No. 21, 30.08.2012, p. 7237-7254.

Research output: Contribution to journalArticle

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