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 language | English (US) |
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Pages (from-to) | 7237-7254 |
Number of pages | 18 |
Journal | Journal of Computational Physics |
Volume | 231 |
Issue number | 21 |
DOIs | |
State | Published - Aug 30 2012 |
Externally published | Yes |
Keywords
- Biopolymers
- Coarse-grained molecular systems
- Long-range interactions
- Multiresolution problems
- Pairwise interactions
- Pseudo-center
- Pseudo-inertia tensor
ASJC Scopus subject areas
- Numerical Analysis
- Modeling and Simulation
- Physics and Astronomy (miscellaneous)
- General Physics and Astronomy
- Computer Science Applications
- Computational Mathematics
- Applied Mathematics