Algorithmic challenges in computational molecular biophysics

DOI10.1006/jcph.1998.6182zbMath0935.92008OpenAlexW2104766043MaRDI QIDQ1305945

John A. jun. Board, Laxmikant V. Kalé, Robert D. Skeel, Axel T. Brunger, Jan Hermans, Tamar Schlick, Klaus Schulten

Publication date: 4 May 2000

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

Full work available at URL: https://semanticscholar.org/paper/033fb232e4c042da3437a656893e10e7b1059c42

zbMATH Keywords

molecular dynamicslong-time integrationbiomolecular simulationscrystallographic refinementfast electrostaticshigh-performance platforms

Mathematics Subject Classification ID

Biophysics (92C05) Computational methods for problems pertaining to biology (92-08) Computer aspects of numerical algorithms (65Y99)

Related Items (12)

Variable order revised binary treecode ⋮ A framework of the harmonic Arnoldi method for evaluating \(\varphi\)-functions with applications to exponential integrators ⋮ Zonal methods for the parallel execution of range-limited \(N\)-body simulations ⋮ A fast mollified impulse method for biomolecular atomistic simulations ⋮ An adaptive fast multipole method in Cartesian basis, enabled by algorithmic differentiation ⋮ The fast multipole method: Numerical implementation ⋮ A simple spectral algorithm for solving large-scale Poisson equation in 2D ⋮ Auxiliary field simulation and Coulomb's law ⋮ Error and timing analysis of multiple time-step integration methods for molecular dynamics ⋮ \(K\)-means clustering for optimal partitioning and dynamic load balancing of parallel hierarchical \(N\)-body simulations ⋮ Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics ⋮ Effective computational strategies for determining structures of carcinogen-damaged DNA

Uses Software

• NAMD
• NAMD2
• VMD

Cites Work

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• Optimization by Simulated Annealing
• RATTLE: A velocity version of the SHAKE algorithm for molecular dynamics calculations
• Ewald summation techniques in perspective: A survey
• Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics
• Reconstructing protentials of mean force through time series analysis of steered molecular dynamics simulations
• NAMD2: Greater scalability for parallel molecular dynamics
• Dangers of multiple time step methods
• Symplectic numerical integrators in constrained Hamiltonian systems
• Nonlinear resonance artifacts in molecular dynamics simulations
• A fast recursive algorithm for molecular dynamics simulation
• A multipole-based algorithm for efficient calculation of forces and potentials in macroscopic periodic assemblies of particles
• An Implementation of the Fast Multipole Method without Multipoles
• Long-Time-Step Methods for Oscillatory Differential Equations
• An Iterative PPPM Method for Simulating Coulombic Systems on Distributed Memory Parallel Computers
• Equation of State Calculations by Fast Computing Machines
• A fast algorithm for particle simulations

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