free-energy

There are 5 repositories under free-energy topic.

plumed / plumed2
Development version of plumed 2
c-plus-plus enhanced-sampling free-energy molecular-dynamics plugin plumed plumed2 trajectory-analysis
Language:C++ 323
Colvars / colvars
Collective variables library for molecular simulation and analysis programs
simulation molecular-dynamics free-energy namd vmd lammps enhanced-sampling gromacs tinkerhp collective-variables
Language:C++ 194
alchemistry / alchemlyb
the simple alchemistry library
free-energy library molecular-dynamics python science
Language:Python 183
choderalab / yank
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
molecular-dynamics molecular-dynamics-simulation alchemical-free-energy-calculations drug-discovery free-energy openmm mskcc python alchemical free-energy-perturbation
Language:Python 173
OpenFreeEnergy / openfe
The Open Free Energy toolkit
molecular-dynamics biophysics free-energy-calculations computational-chemistry free-energy
Language:Python 124
HeatPumpController
openhp / HeatPumpController
The Valden Heat Pump controller is a platform to precisely control heat pumps
pcb refrigeration rs-485 green-energy heat-pump heat-exchange controller electronics compressor diy thermostat gerber heating eev txv arduino free-energy renewable-energy household
Language:C++ 121
ngc-learn
NACLab / ngc-learn
NGC-Learn: Neurobiological Learning and Biomimetic Systems Simulation in Python
biological-neural-networks brain-inspired-computing cognitive-science computational-neuroscience credit-assignment credit-assignment-problem free-energy hebbian-learning jax learning-algorithms local-learning machine-learning neural-networks neuroscience predictive-coding predictive-processing python spiking-networks spiking-neural-networks
Language:Python 96
GOMC-WSU / GOMC
GOMC - GPU Optimized Monte Carlo is a parallel molecular simulation code designed for high-performance simulation of large systems
monte-carlo monte-carlo-simulation gpu openmp adsorption free-energy phase-equilibrium surface-tension cuda gibbs-ensemble grand-canonical-monte-carlo
Language:C++ 68
calphy
ICAMS / calphy
A Python library and command line interface for automated free energy calculations
free-energy free-energy-calculations thermodynamic-calculations molecular-dynamics lammps interatomic-potentials
Language:Python 58
markovmodel / molPX
IPython API to visualize MD-trajectories along projected trajectories inside a Jupyter notebook
visualization tica jupyter-notebook ipython-notebook widget molecular-dynamics free-energy
Language:Python 39
tomekkorbak / active-inference
A toy model of Friston's active inference in Tensorflow
deep-learning free-energy cognitive-science tensorflow variational-inference
Language:Jupyter Notebook 39
MDPOW
Becksteinlab / MDPOW
Calculation of water/solvent partition coefficients with Gromacs.
molecular-dynamics free-energy gromacs python gromacswrapper science
Language:Python 23
craabreu / ufedmm
Unified Free Energy Dynamics (UFED) simulations with OpenMM
molecular-dynamics free-energy enhanced-sampling collective-variables metadynamics openmm
Language:Python 22
delemottelab / InfleCS-free-energy-clustering-tutorial
Python tutorial for estimating and clustering free energy landscapes with InfleCS.
clustering free-energy inflecs molecular-dynamics
Language:Jupyter Notebook 21
bio-phys / PyDHAMed
Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations
md-simulations science python free-energy free-energies kinetics kinetic-modeling molecular-dynamics
Language:Jupyter Notebook 19
deepmodeling / dpti
A Python Package to Automate Thermodynamic Integration Calculations for Free Energy
atomistic-simulations free-energy molecular-dynamics workflow thermodynamic-integration
Language:Python 19
evanseitz / ManifoldEM_Python
ManifoldEM Python suite
biomolecule cryo-em embedding free-energy kernel-methods machine-learning manifold-learning manifoldem quantitative-biology spectral-methods
Language:Python 15
mcbal / afem
Implementation of approximate free-energy minimization in PyTorch
artificial-intelligence attention-mechanism boltzmann-machines deep-learning free-energy hopfield-networks ising-spin-models neural-networks partition-functions pytorch saddle-point spin-models statistical-physics steepest-descent transformers
Language:Python 15
SimonBoothroyd / absolv
Absolute solvation free energy calculations with OpenFF and OpenMM
alchemical free-energy hydration non-equilibrium openff openmm solvation
Language:Python 13
ajaymur91 / CLIPS
Fast estimation of ion-pairing for screening electrolytes
cations free-energy free-energy-calculations metadynamics pmf potential-of-mean-force gromacs plumed opes
Language:Shell 12
pierrebaudot / INFOTOPO
Programs for Information Topology Data Analysis
data-analysis data-structure pattern-recognition statistical-learning statistical-mechanics information-topology information-theory information-landscapes entropy mutual-information synergynetwork free-energy complex-systems complex-networks
Language:Python 12
theavey / ParaTemp
A package for molecular dynamics analysis and parallel tempering in GROMACS
molecular-dynamics analysis free-energy gromacs replicas mdanalysis
Language:Python 11
alchemistry / alchemtest
the simple alchemistry test set
science datasets molecular-dynamics free-energy
Language:Python 9
melomcr / QMMM_String_eABF_Tutorial
NAMD QM/MM Tutorial on Free Energy Profile of Reaction Mechanisms
qm-mm jupyter-notebook molecular-dynamics free-energy
Language:Jupyter Notebook 9
craabreu / mics
A friendly Python library for multistate analysis with MICS and MBAR
free-energy statistics molecular-dynamics monte-carlo multistate-bennett-acceptance-ratio mixture-model
Language:Python 7
floWneffetS / tutorial_dcTMD
Tutorial for the usage of the dcTMD approach and Langevin simulations employing the trypsin-benzamidine complex as example.
nonequilibrium-thermodynamics nonequilibrium-physics free-energy friction tutorial physics-simulation biomolecular-simulation
Language:Python 7
evanseitz / ManifoldEM_ESPER
Software implementation for paper Heuristic Analysis of Manifolds from Simulated Cryo-EM Ensemble Data
biomolecule cryo-em embedding free-energy machine-learning manifold-learning quantitative-biology spectral-methods synthetic-data
Language:Python 6
mazpie / contrastive-aif
[NeurIPS 2021] Contrastive learning formulation of the active inference framework, for matching visual goal states.
action-learning active-inference contrastive-learning free-energy world-models
Language:Python 6
charlesdavid / JED
JED is a program for performing Essential Dynamics of protein trajectories written in Java. JED is a powerful tool for examining the dynamics of proteins from trajectories derived from MD or Geometric simulations. Currently, there are two types of PCA: distance-pair and Cartesian, and three models: COV, CORR, and PCORR.
pca-analysis subspace-identification covariance-matrix correlation-matrices essentialmode principal-components dynamical-modeling correlation-measures pymol free-energy kernel-density-estimation eigen-vector-decomposition
Language:HTML 5
POLARIS
evanseitz / POLARIS
Path of least action analysis on energy landscapes
free-energy quantitative-biology cryo-em pathfinding-algorithm
Language:Python 5
Ferg-Lab / pines
Permutationally invariant networks for enhanced sampling (PINES)
collective-variables molecular-simulation enhanced-sampling plumed free-energy permutational-invariance
Language:C++ 5
colombarifm / themis
Software to Assess Association Free Energies via Direct Estimative of Partition Functions
intermolecular-interactions configurational-partition-function free-energy entropy dimer-association reaction-coordinate-calculation
Language:Fortran 4
ggirelli / ood-fish
Orthogonal Oligo Design for Fluorescence In Situ Hybridization (a.k.a. OOD-FISH)
barcode barcodes blat clique dimerization dna dna-sequences free-energy graph-theory pmc sequence sequence-alignments sequencing thermodynamics
Language:R 4
anniewesterlund / InfleCS-free-energy-clustering-tutorial
Python tutorial for estimating and clustering free energy landscapes with InfleCS.
molecular-dynamics clustering tutorial inflecs free-energy
Language:Python 3
craabreu / openxps
Extended Phase-Space Simulations with OpenMM
enhanced-sampling free-energy molecular-dynamics openmm
Language:Python 3
tagtog12000 / GrandPotential
Grand potential (Free energy) in finite temperature many-body perturbation theory
grand-potential free-energy many-body-perturbation-theory finite-temperature
Language:C++ 3