CREST - A program for the automated exploration of low-energy molecular chemical space.
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Updated
Aug 21, 2024 - Fortran
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
Fast estimation of ion-pairing for screening electrolytes
A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling methods using GROMACS
Useful Collective Variables for OpenMM
Python package for efficient analysis of HILLS files generated by Plumed metadynamics simulations. Inspired by the Metadynminer package for R.
Plumology - Tools to analyse biased molecular dynamics simulations
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
A Python package for enhancing VASP AIMD simulations and analysis
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.
Files for PLUMED Masterclass-22-11
Simple tools for obtaining time from biased molecular dynamics simulations
C++ implementation of metadynamics simulation on a potential energy surface
A package to help automate molecular dynamics calculations
Binary classifier as CV in enhanced sampling
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