Efficient force field calculation in articulated multiscale molecular simulations

Mohammad Poursina, Kurt S. Anderson

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Multiscale simulations of molecular systems such as proteins, DNAs, and RNAs are implemented using models with different resolutions ranging from a fully atomistic model to coarse-grained molecules, up to a 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, a novel method is presented to approximate the resultant force and the associated moment for long-range particle-body and body-body interactions applicable to multiresolution coarse-grained simulation of biopolymers. The resultant moment is due to the fact that the net force does not necessarily act through the center of mass of the body. This moment is neglected in bead-based coarse models which use particle dynamics to form the equations of motion of each large spherical pseudo-atom. The presented method significantly reduces the cost of the force field calculations specially in multiscale models which contain rigid subdomains.

Original languageEnglish (US)
Title of host publicationProceedings of the 4th International Conference on Computational Methods for Coupled Problems in Science and Engineering, COUPLED PROBLEMS 2011
Pages325-336
Number of pages12
StatePublished - Dec 1 2011
Event4th International Conference on Computational Methods for Coupled Problems in Science and Engineering, COUPLED PROBLEMS 2011 - Kos, Greece
Duration: Jun 20 2011Jun 22 2011

Publication series

NameProceedings of the 4th International Conference on Computational Methods for Coupled Problems in Science and Engineering, COUPLED PROBLEMS 2011

Other

Other4th International Conference on Computational Methods for Coupled Problems in Science and Engineering, COUPLED PROBLEMS 2011
CountryGreece
CityKos
Period6/20/116/22/11

Keywords

  • Force field
  • Multiscale problems
  • Pseudo-center
  • Pseudo-inertia tensor

ASJC Scopus subject areas

  • Applied Mathematics
  • Computational Mathematics

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  • Cite this

    Poursina, M., & Anderson, K. S. (2011). Efficient force field calculation in articulated multiscale molecular simulations. In Proceedings of the 4th International Conference on Computational Methods for Coupled Problems in Science and Engineering, COUPLED PROBLEMS 2011 (pp. 325-336). (Proceedings of the 4th International Conference on Computational Methods for Coupled Problems in Science and Engineering, COUPLED PROBLEMS 2011).