REACH: A program for coarse-grained biomolecular simulation

Journal Article · Mon Jan 12 23:00:00 EST 2009 · Computer Physics Communications

DOI:https://doi.org/10.1016/j.cpc.2009.01.007· OSTI ID:1376290

Moritsugu, Kei ^[1]; Smith, Jeremy C. ^[2]

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1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Molecular Biophysics
2. RIKEN, Saitama (Japan). Computational Science Research Program

REACH (Realistic Extension Algorithm via Covariance Hessian) is a program package for residue-scale coarse-grained biomolecular simulation. The program calculates the force constants of a residue-scale elastic network model in single-domain proteins using the variance–covariance matrix obtained from atomistic molecular dynamics simulation. Secondary-structure dependence of the force constants is integrated. Finally, the method involves self-consistent, direct mapping of atomistic simulation results onto a coarse-grained force field in an efficient automated procedure without requiring iterative fits and avoiding system dependence.

• Research Organization: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
• Sponsoring Organization: USDOE Laboratory Directed Research and Development (LDRD) Program; European Union (EU)
• DOE Contract Number: AC05-00OR22725
• OSTI ID: 1376290
• Journal Information: Computer Physics Communications, Journal Name: Computer Physics Communications Journal Issue: 7 Vol. 180; ISSN 0010-4655
• Publisher: Elsevier
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
97 MATHEMATICS AND COMPUTING
Coarse-grained force field
Elastic network model (ENM)
Molecular Dynamics (MD) simulation
REACH