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
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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
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Comment Comment on "Using Quaternions to Calculate RMSD" (J. Comp. Chem. 25, 1849 (2004))
TL;DR: Coutsias et al. as discussed by the authors compared the Kabsch method and the quaternion method to find the optimal superposition of two molecular structures, which is based on a representation of rotations by quaternions.
Journal ArticleDOI
Hydrogen motions in defective graphene: the role of surface defects.
Chiara Cavallari,Daniele Pontiroli,Mónica Jiménez-Ruiz,Mark A. Johnson,Matteo Aramini,Mattia Gaboardi,Stewart F. Parker,Mauro Riccò,Stéphane Rols +8 more
TL;DR: This paper combines neutron vibrational spectroscopy with DFT molecular dynamics simulations to study the local environment of H structures chemisorbed at the surface of disordered graphene sheets.
DissertationDOI
On the prediction of thermodynamic properties by atomistic simulation : from vapor-liquid equilibrium of alcohols to self-assembly in mixed solvents
TL;DR: In this article, the authors characterized the thermodynamic signature of perylene bisimide in aqueous solution using molecular dynamics simulations in explicit solvent, with the aim to unravel the impact of temperature, pressure, and solvent composition on the free energy of aggregation and its enthalpic and entropic contributions.
Journal ArticleDOI
Phonons and lithium diffusion in LiAlO 2
Mayanak K. Gupta,Mayanak K. Gupta,Ranjan Mittal,Ranjan Mittal,Baltej Singh,Baltej Singh,Olivier Delaire,Srungarpu N. Achary,Srungarpu N. Achary,Stéphane Rols,Avesh K. Tyagi,Avesh K. Tyagi,Samrath L. Chaplot,Samrath L. Chaplot +13 more
TL;DR: In this paper, the authors investigated phonons and lithium diffusion in the perfect crystalline phase, the vacancy structure, and the amorphous phase, and found that phonon modes related to Li vibrations broaden on warming as reflected in measured phonon density of states (DOS) and reproduced in simulations.
Journal ArticleDOI
Understanding Structural and Transport Properties of Dissolved Li 2 S 8 in Ionic Liquid Electrolytes through Molecular Dynamics Simulations.
TL;DR: In this paper, the authors performed classical molecular dynamics simulations to explore the microscopic mechanism and transport behaviors of typical Li2 S8 species in ionic liquids and ionic liquid-based electrolyte systems.
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