Book ChapterDOI
Thermostat Algorithms for Molecular Dynamics Simulations
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TLDR
A review of the various thermostat algorithms can be found in this article, with a focus on the physical basis, their advantages and their shortcomings, as well as their physical basis.Abstract:
Molecular dynamics simulations rely on integrating the classical (Newtonian) equations of motion for a molecular system and thus, sample a microcanonical (constant- energy) ensemble by default. However, for compatibility with experiment, it is often desirable to sample configurations from a canonical (constant-temperature) ensemble instead. A modi- fication of the basic molecular dynamics scheme with the purpose of maintaining the temper- ature constant (on average) is called a thermostat algorithm. The present article reviews the various thermostat algorithms proposed to date, their physical basis, their advantages and their shortcomings.read more
Citations
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Journal ArticleDOI
Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning.
TL;DR: Since no significant difference in kinetics or thermodynamics is observed by the use of fast HMR trajectories, further evidence is provided that long-time-step HMR MD simulations are a viable tool for accelerating molecular dynamics simulations for molecules of biochemical interest.
Journal ArticleDOI
Thermal conductivity and thermal rectification in graphene nanoribbons: a molecular dynamics study.
TL;DR: In this article, the thermal conductivity of symmetric and asymmetric graphene nanoribbons (GNRs) of several nanometers in size (up to ∼4 nm wide and ∼10 nm long) was calculated.
Journal ArticleDOI
Role of Molecular Dynamics and Related Methods in Drug Discovery.
TL;DR: The theoretical background of MD and enhanced sampling methods is reviewed, focusing on free-energy perturbation, metadynamics, steered MD, and other methods most consistently used to study drug-target binding.
Journal ArticleDOI
The GROMOS software for biomolecular simulation: GROMOS05
Markus Christen,Philippe H. Hünenberger,Dirk Bakowies,Riccardo Baron,Roland Bürgi,Daan P. Geerke,Tim N. Heinz,Mika A. Kastenholz,Vincent Kräutler,Chris Oostenbrink,Christine Peter,Daniel Trzesniak,Wilfred F. van Gunsteren +12 more
TL;DR: The latest version of the Groningen Molecular Simulation program package, GROMOS05, has been developed for the dynamical modelling of (bio)molecules using the methods of molecular dynamics, stochastic dynamics, and energy minimization.
References
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Book
Computer Simulation of Liquids
Michael P. Allen,D. J. Tildesley +1 more
TL;DR: In this paper, the gear predictor -corrector is used to calculate forces and torques in a non-equilibrium molecular dynamics simulation using Monte Carlo methods. But it is not suitable for the gear prediction problem.
Book ChapterDOI
Accounting for molecular mobility in structure determination based on nuclear magnetic resonance spectroscopic and X-ray diffraction data
Wilfred F. van Gunsteren,Roger M. Brunne,Piet Gros,RenéC Van Schaik,Celia A. Schiffer,Andrew E. Torda +5 more
TL;DR: This chapter discusses procedures to obtain an ideal representation of a biomolecule, with an eye to appropriately accounting for molecular mobility and flexibility in structure determination based on nuclear magnetic resonance (NMR) spectroscopic and x-ray diffraction data.