/PySAGES-examples

Repository that showcases examples of the use of PySAGES coupled to a number of MD engines

Primary LanguageJupyter Notebook

PySAGES-examples

Repository containing an extensive set of examples for enhanced sampling simulations using PySAGES.
The repo containing the PySAGES code can be found here.

Repo organization

Examples are divided in two main categories: classic examples and research examples.
The repo is organized as follows:

PySAGES-examples
│   README.md
│
└───backend01
│   │
│   └───classic
│   │   │
│   │   └───system01
│   │   │   │
│   │   │   └───method01
│   │   │   │   │   system01_method01.ipynb
│   │   │   │   │   system01_method01.md
│   │   │   │   │   system01_method01.py
│   │   │   │
│   │   │   └───method02
│   │   │   │   │   system01_method02.ipynb
│   │   │   │   │   system01_method02.md
│   │   │   │   │   system01_method02.py
│   │   │   │
│   │   │   └───method03
│   │   │       │   ...
│   │   │
│   │   └───system02
│   │       │   ...
│   │
│   └───research
│       │
│       └───system01
│       │   │
│       │   └───method01
│       │   │   │   system01_method01.ipynb
│       │   │   │   system01_method01.md
│       │   │   │   system01_method01.py
│       │   │
│       │   └───method02
│       │       │   ...
│       │  
│       └───system02
│           │   ...
│   
└───backend02
│   │   ...
...

where backend?? = ['ase', 'hoomd-blue', 'openmm']; system?? = ['butane', 'alaninedp', 'nacl', etc.]; method?? = ['abf', 'cff', etc.].

Moreover, the folder inputs/ contains some auxiliary files such as starting coordinates.

List of available examples

system method CV script notebook
butane ANN dihedral angle hoomd.py; hoomd3.py butane_ANN
butane CFF dihedral angle hoomd.py; hoomd3.py butane_CFF
butane FUNN dihedral angle hoomd.py; hoomd3.py butane_FUNN
butane Metadynamics dihedral angle hoomd.py; hoomd3.py ---
butane SpectralABF dihedral angle hoomd.py; hoomd3.py butane_SpectralABF
alanine dp ABF 2 x dihedral angle openmm.py ---
alanine dp ANN 2 x dihedral angle openmm.py ---
alanine dp CFF 2 x dihedral angle openmm.py ---
alanine dp FUNN 2 x dihedral angle openmm.py ---
alanine dp Metadynamics 2 x dihedral angle openmm.py adp_Metadynamics
alanine dp SpectralABF 2 x dihedral angle openmm.py adp_SpectralABF
alanine dp unbiased 2 x dihedral angle openmm.py ---

ANN = Artificial Neural Network sampling; FUNN = adaptive Force-biasing sampling Using Neural Networks, or FUNN-ABF; CFF = Combined Force-Frequency sampling; SpectralABF = Spectral Adaptive Biasing Force.

See the PySAGES manuscript for more info on the methods and their citations.