A fast mollified impulse method for biomolecular atomistic simulations

DOI10.1016/J.JCP.2016.12.024MaRDI QIDQ1685170zbMATH OpenOpenAlexFDO

Authors L. Fath, Marlis Hochbruck, Chandra Veer Singh

Publication date 13 December 2017

Published in Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jcp.2016.12.024

zbMATH Keywords

corotationhighly oscillatorymolecular dynamicsmollified impulse methodresonances

Mathematics Subject Classification ID

Biomechanical solid mechanics (74L15) Biochemistry, molecular biology (92C40)

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Cites work

• A fast recursive algorithm for molecular dynamics simulation
• Algorithmic challenges in computational molecular biophysics
• Dangers of multiple time step methods
• Fast parallel algorithms for short-range molecular dynamics
• Geometric Numerical Integration
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• scientific article; zbMATH DE number 1405381 (Why is no real title available?)
• scientific article; zbMATH DE number 5171040 (Why is no real title available?)
• Implementing molecular dynamics on hybrid high performance computers-short range forces
• Long-Time-Step Methods for Oscillatory Differential Equations
• Molecular modeling and simulation. An interdisciplinary guide.
• Mollified Impulse Methods for Highly Oscillatory Differential Equations
• Multiple time scales in classical and quantum-classical molecular dynamics
• Nonlinear resonance artifacts in molecular dynamics simulations
• Overcoming instabilities in Verlet-I/r-RESPA with the mollified impulse method
• RATTLE: A velocity version of the SHAKE algorithm for molecular dynamics calculations
• Simulating Hamiltonian Dynamics
• Targeted Mollified Impulse: A Multiscale Stochastic Integrator for Long Molecular Dynamics Simulations
• Verlet-I/R-RESPA/Impulse is Limited by Nonlinear Instabilities

Cited in

(2)

• Targeted Mollified Impulse: A Multiscale Stochastic Integrator for Long Molecular Dynamics Simulations
• Fast iterative method for local steric Poisson-Boltzmann theories in biomolecular solvation

Describes a project that uses

Uses Software

• CHARMM
• OVITO
• VMD

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