This program computes statistical quantities over a Molecular Dynamics TRAJectory.
This code is not bug-free, nor extensively and accurately tested by the author.
- Main code: Basic C++ compiler and libraries.
- Python utilities: python3 with few libraries: numpy, scipy, matplotlib.
Clone or Download this repository, install the path and compile with make:
gh repo clone flagiu/mdtraj
cd mdtraj/version/
bash ./install_path.sh
makewhere 'version' can be:
- 'notype' (mono-species);
- 'mixture' (mono- or multi-species);
The best maintained version is currently 'mixture'.
Run helper message for instructions:
path-to-this-repo/version/bin/mdtraj -hMost of the input comes from the command line, except some features requiring parameters files (e.g. see the -rcut command).
The subfolders python/ and shell/ contain some utility scripts (to be used before/after the main program) for plotting or extra calculations. Default units are: Angstrom, picoseconds.
The subfolder examples/ contains some example of application to real or toy systems:
- (notype) LJ particles in different 3d cell shapes: cubic, orthorombic, triclinic.
- (both) Toy particles displaced along a 3d cubic lattice with small random gaussian noise.
- (mixture) Binary LJ mixture.
- (mixture) Short sample of a Phase-Change Heterostructure.
- (mixture) Water molecules.
- (mixture) Logarithmic timestep.
Some limitations of the current version are:
- different frames should have the same number of particles
- S(q) and S(q,t) make sense for cubic boxes only; and they deal with particles as monospecies, ignoring their type.
- S(q),S(q,t) with non-cubic boxes?
- S(q),S(q,t) with mixtures? How? Weighted by mass?
- Add more input formats? GROMACS, ...
- Add structural quasi-entropy? [Oganov,Valle,2008]
- Add crystalline clusters analysis like pyscal?
The development of this code was supported by the ICSC - Centro Nazionale di Ricerca in High Performance Computing, Big Data, and Quantum Computing funded by the European Union - NextGenerationEU.