nMOLDYN: A program package for a neutron scattering oriented analysis of Molecular Dynamics simulations

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. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 657–667, 2003

[1]  Gerald R. Kneller,et al.  The polarized density of states of crystalline polyacetylene. Molecular dynamics analysis and comparison with neutron scattering results , 1993 .

[2]  William H. Press,et al.  Numerical recipes , 1990 .

[3]  Wolfgang Doster,et al.  Methyl group dynamics in the crystalline alanine dipeptide: A combined computer simulation and inelastic neutron scattering analysis , 1992 .

[4]  Gerald R. Kneller,et al.  nMOLDYN: A program package for a neutron scattering oriented analysis of Molecular Dynamics simulations , 1995 .

[5]  S. W. Lovesey,et al.  Theory of neutron scattering from condensed matter , 1984 .

[6]  Gerald R. Kneller,et al.  Superposition of molecular structures using quaternions , 1991 .

[7]  M. E. Rose.  Elementary Theory of Angular Momentum , 1957 .

[8]  S. Altmann.  Rotations, Quaternions, and Double Groups , 1986 .

[9]  Irene A. Stegun,et al.  Handbook of Mathematical Functions. , 1966 .

[10]  I. R. Mcdonald,et al.  Theory of simple liquids , 1998 .

[11]  E. M.,et al.  Statistical Mechanics , 2021, Manual for Theoretical Chemistry.

[12]  E. Ungureanu,et al.  Molecular Physics , 2008, Nature.

[13]  Konrad Hinsen.  The molecular modeling toolkit: A new approach to molecular simulations , 2000 .

[14]  Ieee Acoustics,et al.  IEEE Transactions on Acoustics, Speech, and Signal Processing , 1974 .

[15]  J C Smith,et al.  Liquid-like side-chain dynamics in myoglobin. , 1994, Journal of molecular biology.

[16]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[17]  John G. Proakis,et al.  Probability, random variables and stochastic processes , 1985, IEEE Trans. Acoust. Speech Signal Process..

[18]  Konrad Hinsen,et al.  Computing memory functions from molecular dynamics simulations , 2001 .

[19]  Papoulis A. Probability, random variables, and stochastic processes. New York: McGraw Hill, 1965 , 2004 .

[20]  Julia S. Higgins,et al.  Polymers and Neutron Scattering , 1997 .

[21]  Anthony J. Stone,et al.  Reorientational Correlation Functions, Quaternions and Wigner Rotation Matrices , 1989 .

[22]  K. S. Singwi,et al.  Theory of Slow Neutron Scattering by Liquids. I , 1962 .

[23]  R.N. Bracewell,et al.  Signal analysis , 1978, Proceedings of the IEEE.

[24]  L. Reichl.  A modern course in statistical physics , 1980 .

[25]  William H. Press,et al.  Numerical Recipes in C, 2nd Edition , 1992 .

[26]  Michael Brereton,et al.  A Modern Course in Statistical Physics , 1981 .

[27]  J. Huisman.  The Netherlands , 1996, The Lancet.

[28]  Gerald R. Kneller,et al.  Dynamics of sodium-doped polyacetylene , 1994 .

[29]  William H. Press,et al.  Numerical recipes in C , 2002 .

[30]  Gerald R. Kneller,et al.  Dynamics of alkane chains included in an organic matrix: Molecular dynamics simulation and comparison with neutron scattering experiment , 1998 .

[31]  G. Kneller,et al.  Quaternions as a tool for the analysis of molecular systems , 1991 .

[32]  J. Banavar,et al.  Computer Simulation of Liquids , 1988 .

[33]  Geoffrey M. Davis,et al.  NetCDF User''s Guide for C , 1997 .

[34]  Gerald R. Kneller,et al.  Inelastic neutron scattering from classical systems , 1994 .

[35]  M. Bee,et al.  Quasielastic Neutron Scattering, Principles and Applications in Solid State Chemistry, Biology and Materials Science , 1988 .

[36]  J. Makhoul,et al.  Linear prediction: A tutorial review , 1975, Proceedings of the IEEE.

[37]  Alan R. Jones,et al.  Fast Fourier Transform , 1970, SIGP.

[38]  A. Dianoux,et al.  Microscopic structure and dynamics of liquids , 1978 .