free-energy-calculations
There are 39 repositories under free-energy-calculations topic.
choderalab/openmmtools
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
OpenFreeEnergy/openfe
The Open Free Energy toolkit
proteneer/timemachine
Differentiate all the things!
molmod/psiflow
scalable molecular simulation
OpenBioSim/biosimspace
An interoperable Python framework for biomolecular simulation.
ICAMS/calphy
A Python library and command line interface for automated free energy calculations
OpenBioSim/sire
Sire Molecular Simulations Framework
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
OpenFreeEnergy/kartograf
This package contains tools for setting up hybrid-topology FE calculations
cbc-univie/transformato
Set up relative free energy calculations using a common scaffold
wehs7661/boltzmann_generators
A repository for the final project implementing/applying Boltzmann generators for Computational Statistical Physics (PHYS 7810) at CU Boulder
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.
OpenFreeEnergy/konnektor
Algorithms for various Network Layouts and Tooling for planning FE Calculations
wehs7661/ensemble_md
A python package for performing GROMACS simulation ensembles
wehs7661/enhanced_sampling_tutorials
A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling methods using GROMACS
wehs7661/REMD_analysis
A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations
ajaymur91/CLIPS
Fast estimation of ion-pairing for screening electrolytes
wiederm/endstate_correction
Endstate corrections from MM to QML potential
jhenin/SAFEP_tutorial
A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD
choderalab/yank-benchmark
Standard experimental accuracy benchmark set for YANK.
langevinmodel/folie
Finding Optimal Langevin Inferred Equations
danieljsharpe/metadynamics
C++ implementation of metadynamics simulation on a potential energy surface
ucm-lbqc/polypharm
A Python-based library to perform IFD and MM/GBSA calculations on different targets using a polypharmacological approach.
SalapakaLab-SIMBioSys/Non-Equilibrium-Toolbox
Toolkit for quantifying errors in non-equilibrium data
floWneffetS/dcTMD_scripts_v1.0
Python scripts for the application of dissipation-corrected targeted molecular dynamics analysis.
kuroonai/cowboe
Construction of windows based on free energy. This module has the "cowboe" algorithm which can be used for parameter selection with umbrella sampling.
SHervoe-Hansen/PEO_solubility_in_urea
SI for polyethylene glycol solvation in urea solutions
SHervoe-Hansen/SI-Cavity-Formation
SI for the article named "Free-energy decomposition of salt effects on the solubilities of small molecules and the role of excluded-volume effects"
SHervoe-Hansen/SI-Excluded-Volume-Formation
SI for the article named "Free-energy decomposition of salt effects on the solubilities of small molecules and the role of excluded-volume effects"
Peppone98/Simulations_Recoverin
Standard molecular dynamics and metadynamics simulations of the Recoverin protein. Master's degree thesis @ Unitn
SHervoe-Hansen/PEO_solubility_in_NaCl
SI for polyethylene glycol solvation in NaCl solutions
tsingebrigtsen/FreeEnergyCalculation
RUMD scripts for free-energy calculations of atomic mixtures, rigid molecules, and atomic solids
VirajBhatt9/Excess-chemical-potential-estimation
In this project, for a Lennard Jones fluid, the excess chemical potential is estimated using the finite difference thermodynamic integration method.
samuelhoover/free-energy-minimization
N-dimensional free energy minimization script written in Python.