References ========== .. [nMOLDYN_ref1] nMOLDYN: A program package for a neutron scattering oriented analysis of Molecular Dynamics simulations G. R. Kneller, V. Keiner, M. Kneller, M. Schiller Comp. Phys. Comm. 91, 191-214 (1995) `10.1016/0010-4655(95)00048-K `_ .. [nMOLDYN_ref2] nMoldyn: A program package for a neutron scattering oriented analysis of Molecular Dynamics simulations T. Róg, K. Murzyn, K. Hinsen, G. R. Kneller J. Comput. Chem. 24, 657-667 (2003) `10.1002/jcc.10243 `_ .. [nMOLDYN_ref3] nMoldyn3: Using task farming for a parallel spectroscopy-oriented analysis of molecular dynamics simulations K. Hinsen, E. Pellegrini, S. Stachura, G. R. Kneller J. Comput. Chem. 33, 2043-2048 (2012) `10.1002/jcc.23035 `_ .. [nMOLDYN_ref4] nMoldyn - Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions V. Calandrini, E. Pellegrini, P. Calligari, K. Hinsen, G. R. Kneller JDN 12, 201-232 (2011) `10.1051/sfn/201112010 `_ .. [Ref1] G. Goret, B. Aoun, and E. Pellegrini, “MDANSE: An Interactive Analysis Environment for Molecular Dynamics Simulations,” *J. Chem. Inf. Model.*, vol. 57, no. 1, pp. 1-5, Jan. 2017, `DOI: 10.1021/acs.jcim.6b00571 `_. .. [Ref2] “MDANSE GitHub Actions.” https://github.com/ISISNeutronMuon/MDANSE/actions. .. [Ref3] “Open a Mac app from an unidentified developer.” https://support.apple.com/en-gb/guide/mac-help/mh40616/mac). .. [Ref4] K. Haslam, “How to open a Mac app from an unidentified developer.” https://www.macworld.co.uk/how-to/mac-app-unidentified-developer-3669596/. .. [Ref5] “MDANSE GitHub Issue #8.” https://github.com/ISISNeutronMuon/MDANSE/issues/8. .. [Ref6] “University Corporation for Atmospheric Research.” http://www.ucar.edu/. .. [Ref7] “The HDF Group.” https://www.hdfgroup.org/. .. [Ref9] “MDANSE GitHub Issues.” https://github.com/ISISNeutronMuon/MDANSE/issues. .. [Ref10] F. J. Harris, “On the use of windows for harmonic analysis with the discrete Fourier transform,” *Proc. IEEE*, vol. 66, no. 1, pp. 51–83, 1978, doi: 10.1109/PROC.1978.10837. .. [Ref11] J. P. Boon and S. Yip, *Molecular Hydrodynamics*. New York: McGraw-Hill, 1980. .. [Ref12] G\. R\. Kneller, “Technical Report Jül 2215,” Jülich, Germany. .. [Ref13] A. G. Redfield, “On the Theory of Relaxation Processes,” *IBM J. Res. Dev.*, vol. 1, no. 1, pp. 19–31, 1957, doi: 10.1147/rd.11.0019. .. [Ref14] G. Lipari and A. Szabo, “Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity,” *J. Am. Chem. Soc.*, vol. 104, no. 17, pp. 4546–4559, Aug. 1982, doi: 10.1021/ja00381a009. .. [Ref15] G. Lipari and A. Szabo, “Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results,” *J. Am. Chem. Soc.*, vol. 104, no. 17, pp. 4559–4570, Aug. 1982, doi: 10.1021/ja00381a010. .. [Ref16] L. Van Hove, “Correlations in Space and Time and Born Approximation Scattering in Systems of Interacting Particles,” *Phys. Rev.*, vol. 95, no. 1, pp. 249–262, Jul. 1954, doi: 10.1103/PhysRev.95.249. .. [Ref17] P. Schofield, “Space-Time Correlation Function Formalism for Slow Neutron Scattering,” *Phys. Rev. Lett.*, vol. 4, no. 5, pp. 239–240, Mar. 1960, doi: 10.1103/PhysRevLett.4.239. .. [Ref18] G. R. Kneller, “Inelastic neutron scattering from classical systems,” *Mol. Phys.*, vol. 83, no. 1, pp. 63–87, Sep. 1994, doi: 10.1080/00268979400101081. .. [Ref19] J.-. P. Hansen and I. R. McDonald, “Correlations in Space and Time,” in *Theory of Simple Liquids*, 3rd ed., Elsevier, 2006, pp. 195–201. .. [Ref20] S. W. Lovesey, *Theory of Neutron Scattering from Condensed Matter*, vol. 1. Oxford: Clarendon Press, 1986. .. [Ref21] G. R. Kneller, W. Doster, M. Settles, S. Cusack, and J. C. Smith, “Methyl group dynamics in the crystalline alanine dipeptide: A combined computer simulation and inelastic neutron scattering analysis,” *J. Chem. Phys.*, vol. 97, no. 12, pp. 8864–8879, Dec. 1992, doi: 10.1063/1.463361. .. [Ref22] A. Rahman, K. S. Singwi, and A. Sjölander, “Theory of Slow Neutron Scattering by Liquids. I,” *Phys. Rev.*, vol. 126, no. 3, pp. 986–996, May 1962, doi: 10.1103/PhysRev.126.986. .. [Ref23] J.-P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, “Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes,” *J. Comput. Phys.*, vol. 23, no. 3, pp. 327–341, 1977, doi: https://doi.org/10.1016/0021-9991(77)90098-5. .. [Ref24] G. R. Kneller, “Superposition of Molecular Structures using Quaternions,” *Mol. Simul.*, vol. 7, no. 1–2, pp. 113–119, May 1991, doi: 10.1080/08927029108022453. .. [Ref25] S. L. Altmann, *Rotations, quaternions, and double groups*. Oxford: Clarendon Press, 1986. .. [Ref26] “Axonometric Projection.” https://en.wikipedia.org/wiki/Axonometric_projection#:~:text=In trimetric projection%2C the direction,by the angle of viewing. .. [Ref27] “CASTEP.” http://www.castep.org/. .. [Ref28] “CHARMM.” http://www.charmm.org/. .. [Ref29] “PDB specification.” http://www.wwpdb.org/documentation/file-format.php. .. [Ref30] “DFTB.” https://dftb.org/. .. [Ref31] “Materials Studio.” https://www.3ds.com/products-services/biovia/products/molecular-modeling-simulation/biovia-materials-studio/. .. [Ref32] “DL_POLY.” https://www.sc.stfc.ac.uk/software/type/computational-materials-and-molecular-science/?searchquery=dl_poly#. .. [Ref33] “Gromacs.” https://www.gromacs.org/. .. [Ref34] “LAMMPS.” https://www.lammps.org/. .. [Ref35] “NAMD.” http://www.ks.uiuc.edu/Research/namd/. .. [Ref36] M. Abramowitz and I. A. Stegun, *Handbook of Mathematical Functions*. New York: Dover, 1972. .. [Ref37] “Interpolations for imshow.” https://matplotlib.org/stable/gallery/images_contours_and_fields/interpolation_methods.html. .. [Ref38] “MDANSE GitHub.” https://github.com/ISISNeutronMuon/MDANSE. .. [Ref39] “Miniconda Windows.” https://docs.conda.io/en/latest/miniconda.html. .. [Ref40] “Microsoft Visual Studio 2008.” http://download.microsoft.com/download/8/1/d/81d3f35e-fa03-485b-953b-ff952e402520/VS2008ProEdition90dayTrialENUX1435622.iso. .. [Ref41] C. Gohlke, “Unofficial Windows Binaries for Python Extension Packages.” https://www.lfd.uci.edu/~gohlke/pythonlibs/#wxpython. .. [Ref42] “Conda MacOS.” https://docs.conda.io/projects/conda/en/latest/user-guide/install/macos.html. .. [Ref43] “CP2K Open Source Molecular Dynamics.” https://www.cp2k.org .. [Ref44] Brigham, E.O. "The Fast Fourier Transfrom" Prentice Hall, Englewood Cliffs (NJ) USA, 1974. .. [Ref45] Papoulis, A. "Signal Analysis" McGraw-Hill, Singapore, 1984. .. [Ref46] Harris, F.J. "Proc. IEEE" (1978), 66 *1*, 51-83. .. [Ref47] Fernandez-Alonso, F. and Price, D. "Neutron Scattering (Experimental Methods in the Physical Sciences)" ISBN: 9780123983749