nMoldyn - Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions
Vania Calandrini,E. Pellegrini,Paolo Calligari,Konrad Hinsen,Gerald R. Kneller,Gerald R. Kneller +5 more
- Vol. 12, pp 201-232
Reads0
Chats0
TLDR
A synoptic view of the range of applications of the latest version of nMoldyn is presented, which includes new modules for a simulation-based interpretation of data from nuclear magnetic resonance spectroscopy, far infraredSpectroscopy and for protein secondary structure analysis.Abstract:
This article gives an introduction into the program nMoldyn, which has been originally conceived to support the interpretation of neutron scattering experiments on complex molecular systems by the calculation of appropriate time correlation functions from classical and quantum molecular dynamics simulations of corresponding model systems. Later the functionality has been extended to include more advanced time series analyses of molecular dynamics trajectories, in particular the calculation of memory functions, which play an essential role in the theory of time correlation functions. Here we present a synoptic view of the range of applications of the latest version of nMoldyn, which includes new modules for a simulation-based interpretation of data from nuclear magnetic resonance spectroscopy, far infrared spectroscopy and for protein secondary structure analysis.read more
Citations
More filters
Signal analysis
TL;DR: The parts of this book of most interest and value to the EMC engineer will be the chapters on Thermal Noise, Antennas, Propagation and Transmission Lines, and Reflection and Refraction.
Journal ArticleDOI
TRAVIS-A free analyzer for trajectories from molecular simulation.
TL;DR: Nine years after the original publication of TRAVIS, some of the recent new functions and features are highlighted, which contribute to make trajectory analysis more efficient.
Journal ArticleDOI
freud: A software suite for high throughput analysis of particle simulation data
Vyas Ramasubramani,Bradley D. Dice,Eric S. Harper,Matthew Spellings,Joshua A. Anderson,Sharon C. Glotzer +5 more
TL;DR: The freud Python package provides the core tools for finding particle neighbors in periodic systems, and offers a uniform API to a wide variety of methods implemented using these tools, enabling analysis of a broader class of data ranging from biomolecular simulations to colloidal experiments.
Journal ArticleDOI
Divergent Diffusion Coefficients in Simulations of Fluids and Lipid Membranes
Martin Vögele,Gerhard Hummer +1 more
TL;DR: The dependence of single-particle diffusion coefficients on the size and shape of the simulation box in molecular dynamics simulations of fluids and lipid membranes is investigated and it is found that the diffusion coefficients of lipids and a carbon nanotube embedded in a lipid membrane diverge with the logarithm of the box width.
References
More filters
Journal Article
Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules
Book
Introduction to modern statistical mechanics
David Chandler,Jerome K. Percus +1 more
TL;DR: In this paper, the fundamentals conditions for equilibrium and stability of non-equilibrium systems are defined. And the Monte Carlo method in statistical mechanics is used for non-interacting (ideal) systems.
Book
Nonequilibrium statistical mechanics
TL;DR: The paradoxes of irreversibility as mentioned in this paper is a well-known problem in nonlinear problems, and it has been studied extensively in the literature for a long time, e.g. in the context of projection operators.
Journal ArticleDOI
Correlations in Space and Time and Born Approximation Scattering in Systems of Interacting Particles
TL;DR: In this paper, a natural time-dependent generalization for the well-known pair distribution function $g(mathrm{r})$ of systems of interacting particles is given, which gives rise to a very simple and entirely general expression for the angular and energy distribution of Born approximation scattering by the system.
Related Papers (5)
Generalized Gradient Approximation Made Simple
System-Size Dependence of Diffusion Coefficients and Viscosities from Molecular Dynamics Simulations with Periodic Boundary Conditions
In-Chul Yeh,Gerhard Hummer +1 more