nMoldyn - Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions

V. Calandrini; E. Pellegrini; P. Calligari; K. Hinsen; G.R. Kneller

doi:10.1051/sfn/201112010

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Volume 12 (2011)

10.1051/sfn/201112010

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Numéro		JDN Volume 12, 2011 JDN 18 - Neutrons et Simulations


Page(s)		201 - 232
Section		From the Atomic Level Characterisation to Coarse-Grained Descriptions
DOI		https://doi.org/10.1051/sfn/201112010
Publié en ligne		9 juin 2011

Collection SFN 12 (2011) 201-232

nMoldyn - Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions

V. Calandrini¹^,2^,6, E. Pellegrini³, P. Calligari⁴, K. Hinsen¹^,2 and G.R. Kneller¹^,2^,5

¹ Centre de Biophysique Moléculaire, CNRS, Rue Charles Sadron, 45071 Orléans, France
² Synchrotron Soleil, L’Orme de Merisiers, 91192 Gif-sur-Yvette, France
³ Institut Laue-Langevin, BP. 156, 6, rue Jules Horowitz, 38042 Grenoble Cedex 9, France
⁴ Département de Chimie, associé au CNRS, École Normale Supérieure, 24 rue Lhomond, 75231 Paris Cedex 05, France
⁵ Université d’Orléans, Château de la Source, Av. du Parc Floral, 45067 Orléans, France
⁶ Centre de Physique Théorique, CNRS, Campus de Luminy, 13288 Marseille, France

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.