A fast mollified impulse method for biomolecular atomistic simulations

DOI10.1016/J.JCP.2016.12.024zbMATH Open1375.92022OpenAlexW2562981926MaRDI QIDQ1685170FDOQ1685170

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

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zbMATH Keywords

resonancesmolecular dynamicshighly oscillatorycorotationmollified impulse method

Mathematics Subject Classification ID

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

Cites Work

• Fast parallel algorithms for short-range molecular dynamics
• Geometric Numerical Integration
• Simulating Hamiltonian Dynamics
• Long-Time-Step Methods for Oscillatory Differential Equations
• Molecular modeling and simulation. An interdisciplinary guide.
• Algorithmic challenges in computational molecular biophysics
• RATTLE: A velocity version of the SHAKE algorithm for molecular dynamics calculations
• Nonlinear resonance artifacts in molecular dynamics simulations
• A fast recursive algorithm for molecular dynamics simulation
• Title not available (Why is that?)
• Implementing molecular dynamics on hybrid high performance computers-short range forces
• Mollified Impulse Methods for Highly Oscillatory Differential Equations
• Verlet-I/R-RESPA/Impulse is Limited by Nonlinear Instabilities
• Dangers of multiple time step methods
• Multiple time scales in classical and quantum-classical molecular dynamics
• Title not available (Why is that?)
• Overcoming instabilities in Verlet-I/r-RESPA with the mollified impulse method
• Title not available (Why is that?)
• Title not available (Why is that?)
• Title not available (Why is that?)
• Targeted Mollified Impulse: A Multiscale Stochastic Integrator for Long Molecular Dynamics Simulations

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

Uses Software

• CHARMM
• OVITO
• VMD

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