ArticleJournal of chemical theory and computation2012
Equipartition Principle for Internal Coordinate Molecular Dynamics.
Article in Journal of chemical theory and computation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Hamiltonian Monte Carlo with Constrained Molecular Dynamics as Gibbs Sampling.Journal of chemical theory and computation · 2017Article
- Force distribution in a semiflexible loop.Physical review. E · 2016Article
- Internal coordinate molecular dynamics: a foundation for multiscale dynamics.The journal of physical chemistry. B · 2015Article
- GneimoSim: a modular internal coordinates molecular dynamics simulation package.Journal of computational chemistry · 2014Article
- A simple molecular mechanics integrator in mixed rigid body and dihedral angle space.The Journal of chemical physics · 2014Article
- Fixman compensating potential for general branched molecules.The Journal of chemical physics · 2013Article
- Advanced techniques for constrained internal coordinate molecular dynamics.Journal of computational chemistry · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The principle of equipartition of (kinetic) energy for all-atom Cartesian molecular dynamics states that each momentum phase space coordinate on the average has ½kT of kinetic energy in a canonical ensemble. This principle is used in molecular dynamics simulations to initialize velocities, and to calculate statistical properties such as entropy. Internal coordinate molecular dynamics (ICMD) models differ from Cartesian models in that the overall kinetic energy depends on the generalized coordinates and includes cross-terms. Due to this coupled structure, no such equipartition principle holds for ICMD models. In this paper we introduce non-canonical modal coordinates to recover some of the structural simplicity of Cartesian models and develop a new equipartition principle for ICMD models. We derive low-order recursive computational algorithms for transforming between the modal and physical coordinates. The equipartition principle in modal coordinates provides a rigorous method for initializing velocities in ICMD simulations thus replacing the ad hoc methods used until now. It also sets the basis for calculating conformational entropy using internal coordinates.
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Registered trials
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