This project is still under construction!

PyBias is a PLUMED plug-in with an embedded Python interpreter. It is intended for a quick prototyping of enhanced sampling methods. The goal of PyBias is bridge the gap between PLUMED and Python.

PLUMED is a library for free energy calculations with molecular dynamics (MD). The calculations can be performed as a function of various collective variables (CV), using state-of-the-art enhanced sampling methods: metadynamics, parallel-bias metadynamics, etc. PLUMED works with most MD engines.

Python environment has a variety of high-quality numerical algorithm (NumPy, SciPy, SimPy, etc.) and machine learning (scikit-learn, Theano, TensorFlow, etc.) libraries, which can be used to compute bias.

Key Features

  • Can use a system or custom Python interpreter
  • All installed Python modules can be used
  • A built-in Python module to access data from PLUMED
  • No PLUMED re-compilation required

Quick Installation

If your are lucky (i.e. your system has all dependencies), it is just a 5-step process:

git clone
cd plumed-pybias
cmake . -DCMAKE_INSTALL_PREFIX=~/opt/pybias
make install

Working Example

This is not yet functional!

# plumed.dat

# Load PyBias plug-in

# Create a collective variable

# Creat a PyBias action, which executes ""


def bias(coord, force, extra):
    force[:] = 0.
    return 0.


PyBias is released under GNU Lesser General Public License (LGPL v3).