title: nMoldyn: a program package for a neutron scattering oriented analysis of molecular dynamics simulations.
abstract: We present a new implementation of the program nMoldyn, which has been developed for the computation and decomposition of neutron scattering intensities from Molecular Dynamics trajectories (Comp. Phys. Commun 1995, 91, 191-214). The new implementation extends the functionality of the original version, provides a much more convenient user interface (both graphical/interactive and batch), and can be used as a tool set for implementing new analysis modules. This was made possible by the use of a high-level language, Python, and of modern object-oriented programming techniques. The quantities that can be calculated by nMoldyn are the mean-square displacement, the velocity autocorrelation function as well as its Fourier transform (the density of states) and its memory function, the angular velocity autocorrelation function and its Fourier transform, the reorientational correlation function, and several functions specific to neutron scattering: the coherent and incoherent intermediate scattering functions with their Fourier transforms, the memory function of the coherent scattering function, and the elastic incoherent structure factor. The possibility to compute memory function is a new and powerful feature that allows to relate simulation results to theoretical studies.
authors.affiliation: Departament of Biophysics, Institute of Molecular Biology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland.
authors.forename: T
authors.initials: T
authors.lastname: Róg
authors.forename: K
authors.initials: K
authors.lastname: Murzyn
authors.forename: K
authors.initials: K
authors.lastname: Hinsen
authors.forename: G R
authors.initials: GR
authors.lastname: Kneller