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New features in version 3.0

- Installers for MacOS X, Win32 and linux

- A new Graphical interface A brand new graphical interface is implemented with Tk library [24].

- A new plotting engine A brand bew plotting engine is implemented using matplotlib python library [25]. This allows to produce high quality plots directly from nMOLDYN.

- Trajectory converters Some trajectory converters are implemented and made directly accessible from nMOLDYN GUI. Those converters allows the conversion of trajectory coming from Amber9 [26], Chemistry at HARvard Macromolecular Mechanics (CHARMM) [27], DL_POLY [28], MaterialsStudio [29], NAnoscale Molecular Dynamics (NAMD) [32], Vienna Ab-initio Simulation Package (VASP) [34] and X-PLOR [35] to nMOLDYN MMTK trajectory input formats.

- Converter from NetCDF to ASCII A converter from NetCDF to ASCII that wraps ncdump [36] program is implemented.

- Converter from ASCII to NetCDF A converter from ASCII to NetCDF that wraps ncgen [37] program is implemented.

- Pair Distribution Function The Pair-Distribution Function (PDF) analysis is implemented using Pyrex code for a faster analysis.

- Coordination number The Coordination Number (CN) analysis is implemented using Pyrex code for a faster analysis.

- Spatial Density The Spatial Density (SD) analysis is implemented using Pyrex code for a faster analysis.

- Radius Of Gyration The Radius Of Gyration (ROG) analysis is implemented.

- Root Mean Square Displacement The Root Mean-Square Deviation (RMSD) analysis is implemented.

- Center Of Mass Trajectory The Center Of Mass Trajectory (COMT) analysis is implemented. It determines the trajectory of the center of mass of one or several group of atoms.

- Global Motion Filter The Global Motion Filtered Trajectory (GMFT) analysis is implemented. It removes the global translation and rotation degrees of freedom from a trajectory.

- Quasi Harmonic Analysis The Quasi-Harmonic Analysis (QHA) analysis is implemented. It allows for the decomposition of a system into its different modes of vibration.

- Static Coherent Structure Factor The Static Coherent Structure Factor (SCSF) analysis is implemented. It allows for the direct computation of the static coherent structure factor.

- Smoothed Static Coherent Structure Factor The Smoothed Static Coherent Structure Factor (SSCSF) analysis is implemented. It allows for the direct computation of the static coherent structure factor withtout any q-vectorsrandom generation. It is implemented using Pyrex code for a faster analysis.

- Order parameter The Order Parameter (OP) analysis is implemented.

- Order parameter using the contact model The Order Parameter using Contact Model (OPCM) analysis developped by Zhang et al. [73] is implemented.

- ScrewFit analysis The ScrewFit 2D methode developped by Paolo Calligari and Gerald Kneller [38] is implemented.

- Partial terms The partials term for all scattering-related properties are now available.

- A new atom selection engine A brand new and much more powerful atom selection engine is implemented. When setting up an anlysis, it allows for the selection from the GUI of almost any kind of subset.

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