MDToolbox.jl
What is MDToolbox.jl?
MDToolbox.jl is a pure Julia package for molecular dynamics (MD) trajectories analysis and modeling of biomolecules. The package contains functions covering the following types of scientific computations:
- I/O for trajectory, coordinate, and topology files used for MD simulations
- Unique type (TrjArray) for storing and processing MD trajectory data
- Flexible atom selections
- Various structural computations, including the least-squares fitting of structures, atom distances, angles, dihedrals, etc.
- Potential of mean force (PMF) or free energy profile from unbiased MD trajectories
- Statistical estimates (WHAM and MBAR methods) from biased MD trajectories
- Dimensional reductions (Principal Component Analysis, and others)
- Markov state model, etc.
Some functions have been imported to this package from our old MATLAB/Octave toolbox https://github.com/ymatsunaga/mdtoolbox
Citations
In preparation
License
MDToolbox.jl is licensed under the BSD 3-Clause License.
Contents
- Installation
- Input and Output
- TrjArray type
- Atom selection
- Superimpose and RMSD
- Free energy surface from MD data
- WHAM (Weighted Histogram Analysis Method)
- File IO
- Structural computations
- Reductions
- WHAM (Weighted Histogram Analysis Method)
- MBAR (Multistate Bennett acceptance ratio)
- Makorv state models
- Workflow for developers