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	CFF	dihedral angle	hoomd.py; hoomd3.py
butane	FUNN	dihedral angle	hoomd.py; hoomd3.py
butane	Metadynamics	dihedral angle	hoomd.py; hoomd3.py	---
butane	SpectralABF	dihedral angle	hoomd.py; hoomd3.py
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
alanine dp	SpectralABF	2 x dihedral angle	openmm.py
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.