CREST - A program for the automated exploration of low-energy molecular chemical space.

Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..

Using supervised machine learning to build collective variables for accelerated sampling

Sparse Gaussian Process Potentials

Unified Free Energy Dynamics (UFED) simulations with OpenMM

Cryptic pocket prediction using AlphaFold 2

A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling methods using GROMACS

Python package for efficient analysis of HILLS files generated by Plumed metadynamics simulations. Inspired by the Metadynminer package for R.

Fast estimation of ion-pairing for screening electrolytes

Useful Collective Variables for OpenMM

A Python package for enhancing VASP AIMD simulations and analysis

This GitHub repo has folders required for setting up the Molecular Dynamics simulations, Metadynamics simulations, and a description of the post-processing codes that were used in the Patil et. al. PNAS 2021

Plumology - Tools to analyse biased molecular dynamics simulations

How one can use binary classifiers, variational auto-encoder, TICA, PCA, distance and dihedral order parameters as CVs in context of pepsin-like aspartic proteases e.g. BACE1 and plasmepsin-II.

Simple tools for obtaining time from biased molecular dynamics simulations

Files for PLUMED Masterclass-22-11

CPMD Free Energy Surface Reconstruction

C++ implementation of metadynamics simulation on a potential energy surface

A package to help automate molecular dynamics calculations

Run metadynamics simulations and analyse free energy surfaces