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nMoldyn

The Computing for Science (CS) group supports ILL scientists, students and visitors in a number of activities including data analysis, instrument simulation and sample simulation.

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nMoldyn - an interactive analysis program for Molecular Dynamics simulations

nMOLDYN is an interactive analysis program for Molecular Dynamics simulations, including the computation of neutron scattering spectra and a range of analyses related to dynamical and structural aspect of molecular trajectories.


The current release 4.0 of n MOLDYN is an upgrade of the version n MOLDYN 3.0 [1]. It provides an improved an advanced user interface (both graphical/interactive and batch), and can be used as a framework for implementing new analysis modules.

nMOLDYN allows one to calculate several dynamics quantities such as the mean-square displacement, the velocity autocorrelation function as well as its Fourier Transform (the density of states) and its memory functions, the angular velocity autocorrelation function and its Fourier transform, the reorientational correlation function... Moreover it can compute several quantities related to neutron scattering such as the coherent and incoherent intermediate scattering functions with their Fourier transforms and their memory functions, the elastic incoherent structure factor, the static coherent structure factor or the radial distribution function. Additionally, the nMOLDYN package allows one to construct modified trajectories from an in- put trajectory; rigid-body trajectories, in which the internal motions of the molecules (or parts thereof) are eliminated, frequency-filtered trajectories, from which motions outside a specified frequency interval are eliminated, global motion filtered trajectory where the global rotation and translation are removed from the input trajectory ...

All nMOLDYN calculations can be applied to a whole system or to arbitrary subsets. The most common subsets can be selected in the graphical interface, less common selections can be specified by Python code via the command-line interface.

The interface

Repository and documentation

nMoldyn 4 repository

Technical documentation

References

nMoldyn 1.0

Kneller, G. R., Keiner, V., Kneller, M., & Schiller, M. (1995). nMOLDYN: A program package for a neutron scattering oriented analysis of Molecular Dynamics simulations. Computer physics communications, 91(1), 191-214.

nMoldyn 2.0

Róg, T., Murzyn, K., Hinsen, K., & Kneller, G. R. (2003). nMoldyn: a program package for a neutron scattering oriented analysis of molecular dynamics simulations. Journal of computational chemistry, 24(5), 657-667.

nMoldyn 3.0

Hinsen, K., Pellegrini, E., Stachura, S., & Kneller, G. R. (2012). nMoldyn 3: Using task farming for a parallel spectroscopy‐oriented analysis of molecular dynamics simulations. Journal of computational chemistry, 33(25), 2043-2048.


See also

Calandrini, V., Pellegrini, E., Calligari, P., Hinsen, K., & Kneller, G. R. (2011). nMoldyn-Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions. École thématique de la Société Française de la Neutronique, 12, 201-232.