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Karplus M: CHARMM: a program for macromolecular energy minimization and dynamics calculations
CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model buildExpand
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CHARMM: The biomolecular simulation program
CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus onExpand
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Constant pressure molecular dynamics simulation: The Langevin piston method
A new method for performing molecular dynamics simulations under constant pressure is presented. In the method, which is based on the extended system formalism introduced by Andersen, theExpand
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An analysis of the accuracy of Langevin and molecular dynamics algorithms
Analytic expressions for mean squared positions and velocities of a harmonic oscillator are derived for Langevin dynamics algorithms valid in the high and low friction limits, and for the VerletExpand
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OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integrationExpand
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Self-guided Langevin dynamics simulation method
This work presents a self-guided Langevin dynamics simulation method. The guiding force is calculated as a local average of the friction forces during a self-guided Langevin dynamics simulation.Expand
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Langevin dynamics of peptides: The frictional dependence of isomerization rates of N‐acetylalanyl‐N′‐methylamide
The rate constant for the transition between the equatorial and axial conformations of N‐acetylalanyl‐N′‐methylamide has been determined from Langevin dynamics (LD) simulations with no explicitExpand
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New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular Simulation
New atom- and group-based spherical-cutoff methods have been developed for the treatment of nonbonded interactions in molecular dynamics (MD) simulation. A new atom-based method, force switching,Expand
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