A fast mollified impulse method for biomolecular atomistic simulations

DOI10.1016/j.jcp.2016.12.024zbMath1375.92022OpenAlexW2562981926MaRDI QIDQ1685170

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

resonancesmolecular dynamicshighly oscillatorycorotationmollified impulse method

Mathematics Subject Classification ID

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

Uses Software

• CHARMM
• OVITO
• VMD

Cites Work

• Implementing molecular dynamics on hybrid high performance computers-short range forces
• Molecular modeling and simulation. An interdisciplinary guide.
• RATTLE: A velocity version of the SHAKE algorithm for molecular dynamics calculations
• Algorithmic challenges in computational molecular biophysics
• Multiple time scales in classical and quantum-classical molecular dynamics
• Dangers of multiple time step methods
• Fast parallel algorithms for short-range molecular dynamics
• Nonlinear resonance artifacts in molecular dynamics simulations
• A fast recursive algorithm for molecular dynamics simulation
• Simulating Hamiltonian Dynamics
• Mollified Impulse Methods for Highly Oscillatory Differential Equations
• Long-Time-Step Methods for Oscillatory Differential Equations
• Verlet-I/R-RESPA/Impulse is Limited by Nonlinear Instabilities
• Targeted Mollified Impulse: A Multiscale Stochastic Integrator for Long Molecular Dynamics Simulations
• Geometric Numerical Integration
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item

This page was built for publication: A fast mollified impulse method for biomolecular atomistic simulations