pypi.org "molecular dynamics" keyword
View the packages on the pypi.org package registry that are tagged with the "molecular dynamics" keyword.
ovito-stride 0.0.0
STRIDE plugin for OVITO1 version - Latest release: 2 months ago - 14 downloads last month - 0 stars on GitHub - 1 maintainer
pmarlo 0.0.41
Protein Markov State Model Analysis with Replica Exchange6 versions - Latest release: 4 days ago - 642 downloads last month - 0 stars on GitHub - 1 maintainer
Top 6.9% on pypi.org
42 versions - Latest release: about 1 month ago - 3 dependent packages - 5 dependent repositories - 8.71 thousand downloads last month - 90 stars on GitHub - 1 maintainer
atomman 1.5.2
Atomistic Manipulation Toolkit42 versions - Latest release: about 1 month ago - 3 dependent packages - 5 dependent repositories - 8.71 thousand downloads last month - 90 stars on GitHub - 1 maintainer
Top 6.1% on pypi.org
23 versions - Latest release: 12 months ago - 3 dependent packages - 8 dependent repositories - 108 thousand downloads last month - 219 stars on GitHub - 3 maintainers
alchemlyb 2.4.1
the simple alchemistry library23 versions - Latest release: 12 months ago - 3 dependent packages - 8 dependent repositories - 108 thousand downloads last month - 219 stars on GitHub - 3 maintainers
partycls 2.0.2
Unsupervised learning of the structure of particulate systems5 versions - Latest release: almost 2 years ago - 1 dependent repositories - 9 downloads last month - 14 stars on GitHub - 1 maintainer
calorine 2.3.1
A Python library for building and sampling NEP models via the GPUMD package17 versions - Latest release: about 1 year ago - 1 dependent package - 64.7 thousand downloads last month - 14 stars on gitlab.com - 2 maintainers
mdigest 0.1.9
Best practices made easy for analysis of correlated motions from molecular dynamics simulations.11 versions - Latest release: 11 months ago - 50 downloads last month - 31 stars on GitHub - 2 maintainers
gemdat 1.6.2
Generalized Molecular Dynamics Analysis Tool16 versions - Latest release: 5 months ago - 84 downloads last month - 29 stars on GitHub - 2 maintainers
mddatasetbuilder 1.3.10
A script to generate molecular dynamics (MD) datasets for machine learning from given LAMMPS traj...29 versions - Latest release: about 1 year ago - 1 dependent repositories - 68 downloads last month - 40 stars on GitHub - 1 maintainer
easymda 0.3.4
Easy MD Analysis (EMDA) is a Python package created with the aim of providing an easy, yet powerf...7 versions - Latest release: over 1 year ago - 13 downloads last month - 3 stars on GitHub - 1 maintainer
mdtool 0.1.10
tools for md or dft10 versions - Latest release: 5 months ago - 39 downloads last month - 2 stars on GitHub - 1 maintainer
rigidbodyfit 1.2.1
Align biomolecular structures with densities11 versions - Latest release: over 2 years ago - 1 dependent repositories - 57 downloads last month - 1 stars on gitlab.com - 1 maintainer
asyncmd 0.4.1
asyncmd is a library to write concurrent code to run and analyze molecular dynamics simulations u...4 versions - Latest release: about 1 month ago - 393 downloads last month - 18 stars on GitHub - 1 maintainer
md2d 1.2.0
A python module for accurate determination of diffusion coefficient from molecular dynamics2 versions - Latest release: almost 3 years ago - 1 dependent repositories - 8 downloads last month - 21 stars on GitHub - 1 maintainer
waterentropy 1.2.0
Python package for calculating interfacial water entropy from molecular dynamics simulations.6 versions - Latest release: 25 days ago - 939 downloads last month - 4 stars on GitHub - 2 maintainers
pybdynamics 0.0.2
Functions for BD simulations and data-analysis2 versions - Latest release: about 2 years ago - 13 downloads last month - 0 stars on GitHub - 1 maintainer
lammps-step 2025.9.2
A SEAMM plug-in for LAMMPS, a forcefield-based molecular dynamics code.71 versions - Latest release: 4 days ago - 1 dependent repositories - 633 downloads last month - 2 stars on GitHub - 1 maintainer
fennol 2025.5.16
FeNNol: Force-field-enhanced Neural Network optimized library3 versions - Latest release: 4 months ago - 29 downloads last month - 57 stars on GitHub - 1 maintainer
mdanse-gui 1.0.0rc1
MDANSE GUI package - the graphical interface for MDANSE7 versions - Latest release: 2 months ago - 47 downloads last month - 26 stars on GitHub - 1 maintainer
mdanse 2.0.0rc1
MDANSE Core package - Molecular Dynamics trajectory handling and analysis code5 versions - Latest release: 2 months ago - 184 downloads last month - 26 stars on GitHub - 1 maintainer
mdkits 1.0.2
kits for md or dft42 versions - Latest release: about 2 months ago - 134 downloads last month - 2 stars on GitHub - 1 maintainer
cemm-gen 2024.7.23
Cellular Environment Mimicking Model GENerator2 versions - Latest release: about 1 year ago - 17 downloads last month - 9 stars on GitHub - 1 maintainer
chemtrayzer 3.0.0b4
Reaction models from molecular dynamics simulations.2 versions - Latest release: 7 months ago - 40 downloads last month - 2 maintainers
mdpeditor 1.2.5
Edit simulation parameter input files for GROMACS16 versions - Latest release: over 3 years ago - 1 dependent repositories - 86 downloads last month - 1 stars on GitLab.com - 1 maintainer
buildcage 0.0.5
Python script to build cage optimimized by OPLS-AA5 versions - Latest release: over 4 years ago - 7 downloads last month - 1 maintainer
lammps-cython 0.6.2
Pythonic Wrapper to LAMMPS using cython23 versions - Latest release: about 6 years ago - 2 dependent repositories - 121 downloads last month - 1 stars on GitLab.com - 1 maintainer
unrolr 0.5.0.3
Dimensionality reduction method for MD trajectories6 versions - Latest release: over 5 years ago - 1 dependent repositories - 26 downloads last month - 2 stars on GitHub - 1 maintainer
martiniglass 1.1.3
4 versions - Latest release: 5 months ago - 122 downloads last month - 15 stars on GitHub - 1 maintainer
Top 9.2% on pypi.org
5 versions - Latest release: almost 3 years ago - 3 dependent packages - 3 dependent repositories - 5.03 thousand downloads last month - 21 stars on GitHub - 1 maintainer
pygpcca 1.0.4
.. |PyPIdownloads| image:: https://static.pepy.tech/personalized-badge/pygpcca?period=total&units...5 versions - Latest release: almost 3 years ago - 3 dependent packages - 3 dependent repositories - 5.03 thousand downloads last month - 21 stars on GitHub - 1 maintainer
Top 4.4% on pypi.org
35 versions - Latest release: about 1 month ago - 5 dependent packages - 13 dependent repositories - 224 thousand downloads last month - 300 stars on GitHub - 7 maintainers
freud-analysis 3.4.0
Powerful, efficient trajectory analysis in scientific Python.35 versions - Latest release: about 1 month ago - 5 dependent packages - 13 dependent repositories - 224 thousand downloads last month - 300 stars on GitHub - 7 maintainers
gamda 0.5 💰
gamda: GPU-Accelerated Molecular Dynamics Analysis3 versions - Latest release: over 1 year ago - 45 downloads last month - 9,412 stars on GitHub - 1 maintainer
adaptive-sampling 3.0.1
Sampling algorithms for molecular transitions7 versions - Latest release: over 1 year ago - 1 dependent repositories - 75 downloads last month - 20 stars on GitHub - 1 maintainer
Top 3.5% on pypi.org
15 versions - Latest release: about 1 year ago - 3 dependent packages - 13 dependent repositories - 11.5 thousand downloads last month - 30 stars on gitlab.com - 2 maintainers
hiphive 1.3.1
High-order force constants for the masses15 versions - Latest release: about 1 year ago - 3 dependent packages - 13 dependent repositories - 11.5 thousand downloads last month - 30 stars on gitlab.com - 2 maintainers
mechanica 0.0.30.dev4
Interactive physics simulation engine38 versions - Latest release: over 4 years ago - 1 dependent repositories - 221 downloads last month - 1 maintainer
autopoly 0.0.1
AutoPoly1 version - Latest release: over 2 years ago - 24 downloads last month - 1 maintainer
mdahole2 0.5.0
A Python interface for the HOLE suite tools to analyze an ion channel pore or transporter pathway...2 versions - Latest release: 10 months ago - 11.6 thousand downloads last month - 7 stars on GitHub - 1 maintainer
fretlabel 0.2.1
PyMOL plugin to interactively label nucleic acids with fluorophores in silico4 versions - Latest release: 6 months ago - 1 dependent repositories - 17 downloads last month - 5 stars on GitHub - 1 maintainer
Top 4.8% on pypi.org
11 versions - Latest release: about 1 year ago - 4 dependent packages - 9 dependent repositories - 251 thousand downloads last month - 124 stars on GitHub - 1 maintainer
pymatgen-analysis-diffusion 2024.7.15
Pymatgen add-on for diffusion analysis.11 versions - Latest release: about 1 year ago - 4 dependent packages - 9 dependent repositories - 251 thousand downloads last month - 124 stars on GitHub - 1 maintainer
waterdynamics 1.2.0
Analysis of water dynamics in molecular dynamics trajectories and water interactions with other m...5 versions - Latest release: 10 months ago - 11.3 thousand downloads last month - 7 stars on GitHub - 3 maintainers
mrcsmooth 0.2
Downsample cryo-EM densities1 version - Latest release: over 3 years ago - 1 dependent repositories - 9 downloads last month - 1 stars on gitlab.com - 1 maintainer
dynasor 1.1.1
Dynamical structure factors and correlation functions from molecular dynamics trajectories10 versions - Latest release: almost 4 years ago - 1 dependent repositories - 173 downloads last month - 29 stars on gitlab.com - 2 maintainers
pydanamics 0.0.0
Molecular dynamic simulation assistant for beginners1 version - Latest release: over 6 years ago - 1 dependent repositories - 8 downloads last month - 1 maintainer
md-davis 0.4.1
A tool for comparative analysis of molecular dynamics simulations of proteins.4 versions - Latest release: over 3 years ago - 1 dependent repositories - 76 downloads last month - 16 stars on GitHub - 1 maintainer
gmxpy 0.0.5
Wrapping GROMACS by Python for me5 versions - Latest release: over 1 year ago - 29 downloads last month - 1 stars on GitHub - 1 maintainer
dsfinterp 0.1
Cubic Spline Interpolation of Dynamics Structure Factors1 version - Latest release: over 11 years ago - 2 dependent repositories - 9 downloads last month - 0 stars on GitHub - 1 maintainer
franken 0.4.1
Franken fine-tuning scheme for ML potentials19 versions - Latest release: 14 days ago - 220 downloads last month - 19 stars on GitHub - 1 maintainer
simphony-osp-simlammps 4.0.0
LAMMPS wrapper for SimPhoNy1 version - Latest release: almost 3 years ago - 15 downloads last month - 0 stars on GitHub - 1 maintainer
flatgraphene 0.3.6
Generate mono and multilayer graphene geometries10 versions - Latest release: almost 4 years ago - 1 dependent repositories - 35 downloads last month - 3 stars on GitHub - 1 maintainer
quickdynamics 0.0.0
Molecular dynamic simulation assistant for beginners1 version - Latest release: over 6 years ago - 1 dependent repositories - 5 downloads last month - 1 maintainer
radonpy-pypi 0.2.9
RadonPy is a Python library to automate physical property calculations for polymer informatics.4 versions - Latest release: over 1 year ago - 505 downloads last month - 180 stars on GitHub - 1 maintainer
waternetworkanalysis 0.4.0
Set of tools for input preparation for conserved water search from MD trajectories (gromacs, ambe...8 versions - Latest release: over 1 year ago - 46 downloads last month - 17 stars on GitHub - 1 maintainer
rcbs.py 0.2.0
Python package useful for analysing MD trajectories and creating QMMM models built on top of MDAn...7 versions - Latest release: over 2 years ago - 6 downloads last month - 3 stars on GitHub - 1 maintainer
Top 5.6% on pypi.org
3 versions - Latest release: almost 3 years ago - 18 downloads last month - 4 stars on GitHub - 1 maintainer
nanoreactor-processing 1.1.1
Automated evaluation of computational nanoreactor simulations3 versions - Latest release: almost 3 years ago - 18 downloads last month - 4 stars on GitHub - 1 maintainer
Top 10.0% on pypi.org
5 versions - Latest release: over 6 years ago - 3 dependent packages - 2 dependent repositories - 531 downloads last month - 46 stars on GitHub - 3 maintainers
pydiffmap 0.2.0
Library for constructing variable bandwidth diffusion maps5 versions - Latest release: over 6 years ago - 3 dependent packages - 2 dependent repositories - 531 downloads last month - 46 stars on GitHub - 3 maintainers
flashmd 0.1.2
Accelerated molecular dynamics with large-time-step predictions4 versions - Latest release: 3 months ago - 276 downloads last month - 1 maintainer
mdinterface 1.3.0
Build Interface Systems for Molecular Dynamics Simulations4 versions - Latest release: about 2 months ago - 20 downloads last month - 2 stars on gitlab.com - 1 maintainer
vizmdend 1.1.0
AMBER mdend file inspector1 version - Latest release: almost 12 years ago - 2 dependent repositories - 4 downloads last month - 0 stars on GitHub - 1 maintainer
prips 1.4
PRIPS: Python Runtime Interface Plugin of SPONGE5 versions - Latest release: over 1 year ago - 19 downloads last month - 1 maintainer
jmdx 0.0.1
Jax Molecular Dynamics eXtended1 version - Latest release: 3 months ago - 154 downloads last month - 0 stars on GitHub - 1 maintainer
open-moldyn 0.1.0
Tools for molecular dynamics simulation and analysis7 versions - Latest release: over 4 years ago - 1 dependent repositories - 63 downloads last month - 2 stars on GitHub - 2 maintainers
logdensity 0.1.dev0
take the logarithm of a cryo-EM density1 version - Latest release: almost 3 years ago - 10 downloads last month - 0 stars on gitlab.com - 1 maintainer
easysrv 0.0.3
Easy to use State Reversible Vampnet with fit, transform and fittransform methods3 versions - Latest release: over 3 years ago - 1 dependent repositories - 15 downloads last month - 2 stars on GitHub - 1 maintainer
fretraj 0.2.11
Predicting FRET with accessible-contact volumes35 versions - Latest release: 6 months ago - 1 dependent repositories - 452 downloads last month - 9 stars on GitHub - 1 maintainer
sea-urchin 1.0.1
The Electrolyte Machine is a set of Python tools to post-process trajectories from AIMD, MD and m...2 versions - Latest release: 9 months ago - 20 downloads last month - 1 stars on gitlab.com - 1 maintainer
sclmd 0.4.7
Semi-classical Langevin molecular dynamics34 versions - Latest release: almost 3 years ago - 1 dependent repositories - 109 downloads last month - 2 stars on GitHub - 1 maintainer
Top 9.9% on pypi.org
23 versions - Latest release: 2 months ago - 2 dependent packages - 3 dependent repositories - 498 downloads last month - 11 stars on GitHub - 1 maintainer
potentials 0.4.1
API database tools for accessing the NIST Interatomic Potentials Repository: explore and download...23 versions - Latest release: 2 months ago - 2 dependent packages - 3 dependent repositories - 498 downloads last month - 11 stars on GitHub - 1 maintainer
dompap 0.0.5
Simulations of point-like particles in any dimension with any pair potential5 versions - Latest release: over 1 year ago - 31 downloads last month - 0 stars on GitHub - 1 maintainer
fhi-vibes 1.1.0
Fritz Haber Institute Vibrational Simulations14 versions - Latest release: 10 months ago - 1 dependent repositories - 343 downloads last month - 18 stars on gitlab.com - 2 maintainers
synd 0.1.4
Synthetic dynamics for trajectory generation5 versions - Latest release: over 2 years ago - 1 dependent repositories - 15 downloads last month - 3 stars on GitHub - 1 maintainer
cgen2gmx 1.1.0
A small commandline tool for managing forcefield parameters used in molecular dynamics simulations4 versions - Latest release: about 1 year ago - 19 downloads last month - 3 stars on GitHub - 1 maintainer
Top 9.8% on pypi.org
21 versions - Latest release: about 2 months ago - 1 dependent repositories - 1.07 thousand downloads last month - 179 stars on GitHub - 1 maintainer
gromacswrapper 0.9.2
A Python wrapper around the GROMACS tools.21 versions - Latest release: about 2 months ago - 1 dependent repositories - 1.07 thousand downloads last month - 179 stars on GitHub - 1 maintainer
simlearn 1.0.0
Simlearn is a way how to teach/learn about simulations with a joy. PyStar is a main application o...1 version - Latest release: almost 4 years ago - 1 dependent repositories - 12 downloads last month - 0 stars on gitlab.com - 1 maintainer
gmxbatch 0.0.2.dev0
Python tools for writing GROMACS batch scripts1 version - Latest release: over 5 years ago - 1 dependent repositories - 10 downloads last month - 2 stars on gitlab.com - 1 maintainer
conservedwatersearch 0.4.1
Conserved water search is a tool for finding conserved water molecules from MD trajectories.9 versions - Latest release: over 1 year ago - 1 dependent package - 1 dependent repositories - 182 downloads last month - 12 stars on GitHub - 1 maintainer
atsim.potentials 0.4.1
atsim.potentials provides tools for working with pair and embedded atom method potential models i...7 versions - Latest release: over 2 years ago - 3 dependent repositories - 49 downloads last month - 13 stars on GitHub - 1 maintainer
pathsimanalysis 1.2.0
Calculates the geometric similarity of molecular dynamics trajectories using path metrics such as...4 versions - Latest release: 10 months ago - 9.99 thousand downloads last month - 0 stars on GitHub - 3 maintainers
lipyphilic 0.12.1
Analyse MD simulations of lipids with python'19 versions - Latest release: 3 months ago - 1 dependent repositories - 2.32 thousand downloads last month - 31 stars on GitHub - 1 maintainer
coarsify 1.0.3
A Python tool for coarse-graining molecular structures4 versions - Latest release: about 2 months ago - 0 stars on GitHub - 1 maintainer
iprpy 0.11.8
Interatomic Potential Repository Python Property Calculations and Tools13 versions - Latest release: about 1 month ago - 1 dependent repositories - 184 downloads last month - 23 stars on GitHub - 1 maintainer
bemm-gen 2024.10.10
Biomolecular Environment Mimicking Model GENerator2 versions - Latest release: 11 months ago - 20 downloads last month - 9 stars on GitHub - 1 maintainer
mdbenchmark 3.0.1
Quickly generate, start and analyze benchmarks for your molecular dynamics simulations.13 versions - Latest release: almost 5 years ago - 1 dependent repositories - 124 downloads last month - 80 stars on GitHub - 3 maintainers
Related Keywords
molecular-dynamics
20
python
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simulation
16
analysis
13
chemistry
8
physics
8
GROMACS
7
gromacs
6
molecular-dynamics-simulation
6
science
6
atomistic
6
simulations
4
computational-chemistry
4
atomic
4
data-analysis
4
scientific
4
computational chemistry
4
lammps
4
MD
3
AMBER
3
machine learning
3
phonons
3
thermal conductivity
3
thermal transport
3
atom
3
forcefield
3
bioinformatics
3
molecular simulations
3
conserved water
2
Lammps
2
water
2
density-functional-theory
2
density functional theory
2
protein
2
MDAnalysis
2
biochemistry
2
interatomic potential
2
single-molecule
2
FRET
2
PDB
2
dynamics
2
chemical reactions
2
SPONGE
2
Amber
2
mdend
2
energy
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LAMMPS
2
dimensionality reduction
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wrapper
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rdkit
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biosimulation
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biology
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mdanalysis
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qt-gui
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force field
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jax
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2
force constants
2
diffusion
2
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2
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structure
2
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lipids
1
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1
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1
solids
1
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1
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1
liquids
1
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1
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1
inelastic electron scattering
1
python3
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data visualization
1
computational-biology
1
protein-structure
1
lipid
1
path similarity
1
franken
1
potentials
1
simphony
1
Fraunhofer IWM
1
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twisted
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graphene
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graphite
1
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1
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benchmark
1