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

TL;DR: 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.

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### "nMoldyn - Interfacing spectroscopic..." refers background in this paper

...[1] to study the equation of state of model liquids and the pioneering molecular dynamics (MD) study of liquid argon by Rahman, which extended the scope of computer simulations to time dependent phenomena [2]....

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...The lysozyme structure was taken from the Brookhaven protein data bank [28] (code 193L[29]) and hydrogen atoms were added to the structure according to standard criteria concerning the chemical bond structure of amino acids....

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### "nMoldyn - Interfacing spectroscopic..." refers methods in this paper

...To mimic a macroscopic system, periodic boundary conditions have been applied and electrostatic interactions have been computed using the particle mesh Ewald method (PME) [53], with a cut-off of 12 Å....

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### "nMoldyn - Interfacing spectroscopic..." refers methods in this paper

...one obtains finally an approximation for the Fourier spectrum of the ACF of a(t), which is based on the AR model [61, 64],...

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