Awesome Open Source
Search
Programming Languages
Languages
All Categories
Categories
About
Search results for python molecular dynamics
molecular-dynamics
x
python
x
183 search results found
Deepmd Kit
⭐
1,303
A deep learning package for many-body potential energy representation and molecular dynamics
Mdanalysis
⭐
1,154
MDAnalysis is a Python library to analyze molecular dynamics simulations.
Coronavirus
⭐
1,108
Folding@home COVID-19 efforts
Awesome Python Chemistry
⭐
971
A curated list of Python packages related to chemistry
Schnetpack
⭐
688
SchNetPack - Deep Neural Networks for Atomistic Systems
Mdtraj
⭐
519
An open library for the analysis of molecular dynamics trajectories
Nequip
⭐
478
NequIP is a code for building E(3)-equivariant interatomic potentials
Torchmd
⭐
465
End-To-End Molecular Dynamics (MD) Engine using PyTorch
Pyiron
⭐
316
pyiron - an integrated development environment (IDE) for computational materials science.
Hoomd Blue
⭐
298
Molecular dynamics and Monte Carlo soft matter simulation on GPUs.
Pyemma
⭐
292
🚂 Python API for Emma's Markov Model Algorithms 🚂
Prolif
⭐
286
Interaction Fingerprints for protein-ligand complexes and more
Freud
⭐
248
Powerful, efficient particle trajectory analysis in scientific Python.
Torchmd Net
⭐
238
Neural network potentials
Openmmtools
⭐
214
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
Nanoengineer
⭐
210
open-source nanotech CAD
Espresso
⭐
206
The ESPResSo package
Tensormol
⭐
190
Tensorflow + Molecules = TensorMol
Moltemplate
⭐
186
A general cross-platform tool for preparing simulations of molecules and complex molecular assemblies
Lammps Input Files
⭐
181
LAMMPS inputs and data files
Chemlab
⭐
173
The chemistry library you were waiting for
Allegro
⭐
169
Allegro is an open-source code for building highly scalable and accurate equivariant deep learning interatomic potentials
Perses
⭐
163
Experiments with expanded ensembles to explore chemical space
Vde
⭐
161
Variational Autoencoder for Dimensionality Reduction of Time-Series
Alchemlyb
⭐
161
the simple alchemistry library
Mbuild
⭐
156
A hierarchical, component based molecule builder
Gromacswrapper
⭐
154
GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2023 supported).
Yank
⭐
150
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
Timemachine
⭐
134
Differentiate all the things!
Drug Computing
⭐
131
Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.
Molecular Design Toolkit
⭐
131
Notebook-integrated tools for molecular simulation and visualization
Sgdml
⭐
124
sGDML - Reference implementation of the Symmetric Gradient Domain Machine Learning model
Msmbuilder
⭐
124
🏗️ Statistical models for biomolecular dynamics 🏗️
Fftool
⭐
117
Tool to build force field input files for molecular simulation
Iodata
⭐
108
Python library for reading, writing, and converting computational chemistry file formats and generating input files.
Foyer
⭐
105
A package for atom-typing as well as applying and disseminating forcefields
Radonpy
⭐
98
RadonPy is a Python library to automate physical property calculations for polymer informatics.
Dynaphopy
⭐
78
Phonon anharmonicity analysis from molecular dynamics
Pensa
⭐
77
PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.
Openfe
⭐
74
The Open Free Energy toolkit
Vermouth Martinize
⭐
71
Describe and apply transformation on molecular structures and topologies
Pytim
⭐
68
a python package for the interfacial analysis of molecular simulations
Mdbenchmark
⭐
67
Quickly generate, start and analyze benchmarks for molecular dynamics simulations.
Biosimspace
⭐
64
Code and resources for the EPSRC BioSimSpace project.
Dockingpie
⭐
54
A Consensus Docking Plugin for PyMOL
Pwtools
⭐
53
pwtools is a Python package for pre- and postprocessing of atomistic calculations, mostly targeted to Quantum Espresso, CPMD, CP2K and LAMMPS. It is almost, but not quite, entirely unlike ASE, with some tools extending numpy/scipy. It has a set of powerful parsers and data types for storing calculation data.
Physical_validation
⭐
52
Physical validation of molecular simulations
Uf3
⭐
51
UF3: a python library for generating ultra-fast interatomic potentials
Taichimd
⭐
50
Interactive, GPU-accelerated Molecular Dynamics using the Taichi programming language
Sharc
⭐
50
The SHARC molecular dynamics (MD) program suite is an ab initio MD software package developed to study the excited-state dynamics of molecules.
Mlcgmd
⭐
49
[TMLR 2023] Simulate time-integrated coarse-grained MD with multi-scale graph neural networks
Isicle
⭐
49
In silico chemical library engine for high-accuracy chemical property prediction
Biosimspace
⭐
48
An interoperable Python framework for biomolecular simulation.
Calphy
⭐
44
A Python library and command line interface for automated free energy calculations
Wepy
⭐
44
Weighted Ensemble simulation framework in Python
Mlff
⭐
42
Build neural networks for machine learning force fields with JAX
Gdpy
⭐
41
Generating Deep Potential with Python
Symd
⭐
36
N-Dimensional MD engine with symmetry group constraints
Grand
⭐
34
A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.
Mddatasetbuilder
⭐
34
A script to build reference datasets for training neural network potentials from given LAMMPS trajectories.
Pycontact
⭐
34
Analysis of non-covalent interactions in MD trajectories
Molearn
⭐
33
protein conformational spaces meet machine learning
Enspara
⭐
32
Modeling molecular ensembles with scalable data structures and parallel computing
Mdsuite
⭐
32
A post-processing engine for particle simulations
Contact_map
⭐
31
Contact map analysis for biomolecules; based on MDTraj
Aimnet
⭐
31
Atoms In Molecules Neural Network Potential
Pycgtool
⭐
30
Generate coarse-grained molecular dynamics models from atomistic trajectories.
Kinisi
⭐
30
A Python package for estimating diffusion properties from molecular dynamics simulations.
Sportran
⭐
29
A code to estimate transport coefficients from the cepstral analysis of a (multi)variate current stationary time series -- [FKA "thermocepstrum"]
Molpy
⭐
28
[WIP] A data structure used to describe molecules in computational chemistry, just like numpy in data science
Ties_md
⭐
28
Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.
Hoomd Examples
⭐
28
HOOMD-blue example scripts.
Hoomd Tf
⭐
27
A plugin that allows the use of Tensorflow in Hoomd-Blue for GPU-accelerated ML+MD
Lipyphilic
⭐
27
A Python toolkit for the analyis of lipid membrane simulations
Molpx
⭐
27
IPython API to visualize MD-trajectories along projected trajectories inside a Jupyter notebook
Isolde
⭐
27
Interactive molecular dynamics based model building into low-resolution crystallographic and cryo-EM maps
Barnaba
⭐
26
Analyse Nucleic Acids Structure and Simulations with baRNAba
Mdciao
⭐
26
mdciao: Analysis of Molecular Dynamics Simulations Using Residue Neighborhoods
Mispr
⭐
24
A software for automating materials science computations
Encodermap
⭐
24
python library for dimensionality reduction
Mdapy
⭐
23
A simple and fast python library to handle the data generated from molecular dynamics simulations
Mdpow
⭐
22
Calculation of water/solvent partition coefficients with Gromacs.
Ligpargen
⭐
22
Hymd
⭐
21
Massively parallel hybrid particle-field molecular dynamics in Python.
Polymer Molecular Dynamics
⭐
21
Perform high-throughput polymer molecular dynamics simulations with ease
Inductiva
⭐
21
Large scale simulations made simple.
Pnerf
⭐
21
Psiresp
⭐
21
RESP with inter- and intra-molecular constraints in Psi4.
Kif
⭐
20
KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.
Vde_metadynamics
⭐
20
Enhanced protein mutational sampling using time-lagged variational autoencoders
Ufedmm
⭐
20
Unified Free Energy Dynamics (UFED) simulations with OpenMM
Ommprotocol
⭐
20
A command line application to launch molecular dynamics simulations with OpenMM
Pycadd
⭐
19
A python package for computer-aid drug design.
Toy Md
⭐
19
Python code for learning Molecular Dynamics simulations
Tidynamics
⭐
18
A tiny package to compute the dynamics of stochastic and molecular simulations
Mdshare
⭐
18
Get access to our MD data files.
Controlled Peptide Generation
⭐
18
source code for https://arxiv.org/abs/2005.11248 "Accelerating Antimicrobial Discovery with Controllable Deep Generative Models and Molecular Dynamics"
Mdgo
⭐
18
A codebase for classical molecular dynamics (MD) simulation setup and results analysis.
Pydhamed
⭐
17
Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations
Peggenerator
⭐
17
Generate PEG topology for GROMACS and LAMMPS
Related Searches
Python Script (17,224)
Python Docker (14,113)
Python Machine Learning (14,099)
Python Tensorflow (13,736)
Python Deep Learning (13,092)
Python Jupyter Notebook (12,976)
Python Network (11,495)
Python Algorithms (10,033)
Python Pytorch (7,877)
Python Neural (7,444)
1-100 of 183 search results
Next >
Privacy
|
About
|
Terms
|
Follow Us On Twitter
Copyright 2018-2024 Awesome Open Source. All rights reserved.