A conda-smithy repository for vermouth.

Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates

Martini Workshop: Simulating a Minimal Bacterial Cell

OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method

Application to assign secondary structure to proteins

INSert membrANE - A simple, versatile tool for building coarse-grained simulation systems

Describe and apply transformation on molecular structures and topologies

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

AlphaFold Meets Flow Matching for Generating Protein Ensembles

Boltzmann Generators and Normalizing Flows in PyTorch

Implementation of methods to sample from Boltzmann distributions

A repository for the final project implementing/applying Boltzmann generators for Computational Statistical Physics (PHYS 7810) at CU Boulder

Toolkit for free-energy calculation setup/analysis and biomolecular structure handling

Enhanced sampling methods for molecular dynamics simulations

OpenMM is a toolkit for molecular simulation using high performance GPU code.

Google Colab notebooks for running molecular dynamics simulations with GROMACS

An introductory workshop to protein language models

Accurate Neural Network Potential on PyTorch

ANI-1 neural net potential with python interface (ASE)

Training neural network potentials

MoleculeKit: Your favorite molecule manipulation kit

Toolkit for free-energy calculation setup/analysis and biomolecular structure handling

End-To-End Molecular Dynamics (MD) Engine using PyTorch

This library would form a permanent home for reusable components for deep probabilistic programming. The library would form and harness a community of users and contributors by focusing initially o…

Understanding Deep Learning - Simon J.D. Prince

PDBFixer fixes problems in PDB files

Enter Unicode characters using LaTeX notation

Text Replacement Definitions for LaTeX Symbols, works for iOS and macOS.

In silico directed evolution of peptide binders with AlphaFold