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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.
Next: User feedback
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pellegrini eric
2009-10-06