free-energy-calculations 开源项目推荐（51 个）

OpenFreeEnergy /openfe

开放自由能源工具包

choderalab /openmmtools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

proteneer /timemachine

Differentiate all the things!

OpenBioSim /biosimspace

An interoperable Python framework for biomolecular simulation.

molmod /psiflow

scalable molecular simulation

ICAMS /calphy

A Python library and command line interface for automated free energy calculations

OpenBioSim /sire

Sire Molecular Simulations Framework

OpenFreeEnergy /kartograf

This package contains tools for setting up hybrid-topology FE calculations

rinikerlab /reeds

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.

choderalab /neutromeratio

Tautomer ratios in solution

weitse-hsu /boltzmann_generators

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

weitse-hsu /enhanced_sampling_tutorials

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

OpenFreeEnergy /konnektor

Algorithms for various Network Layouts and Tooling for planning FE Calculations

cbc-univie /transformato

Set up relative free energy calculations using a common scaffold

weitse-hsu /ensemble_md

A python package for performing GROMACS simulation ensembles

OpenFreeEnergy /openfe_analysis

Structural analysis tools for OpenFE free energy calculations, built on MDAnalysis.

rinikerlab /restraintmaker

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.

jhenin /SAFEP_tutorial

A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD

weitse-hsu /REMD_analysis

A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations

wiederm /endstate_correction

Endstate corrections from MM to QML potential