A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
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Updated
Aug 24, 2024 - Python
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
Differentiate all the things!
The Open Free Energy toolkit
scalable molecular simulation
An interoperable Python framework for biomolecular simulation.
A Python library and command line interface for automated free energy calculations
Sire Molecular Simulations Framework
This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.
Tautomer ratios in solution
A repository for the final project implementing/applying Boltzmann generators for Computational Statistical Physics (PHYS 7810) at CU Boulder
This is an package contains tools for setting up hybrid-topology FE calculations
Set up relative free energy calculations using a common scaffold
Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation technique with coordinate-based particles). It can be used on a script layer or as an interactive plugin for PyMol. Features are different selection modes and Optimizers to distribute restraints.
A python package for performing GROMACS simulation ensembles
Fast estimation of ion-pairing for screening electrolytes
A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations
A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling methods using GROMACS
Endstate corrections from MM to QML potential
A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD
Standard experimental accuracy benchmark set for YANK.
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