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entity-trajectory

Here are 26 public repositories matching this topic...

Scindices / openmm--openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

status-active lang-python lang-cpp role-framework entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-physics domain-molecular-simulation entity-trajectory interface-gpu lang-cuda ecosystem-openmm task-md-engine

Updated Jul 27, 2026
C++

Scindices / lammps--lammps

Public development project of the LAMMPS MD software package

status-active lang-python lang-cpp interface-cli role-framework entity-small-molecule interface-api status-published status-packaged-conda scope-focused method-physics domain-molecular-simulation entity-trajectory interface-gpu lang-cuda entity-crystal task-md-engine domain-materials

Updated Jul 28, 2026
C++

Scindices / torchmd--torchmd

End-To-End Molecular Dynamics (MD) Engine using PyTorch

status-active lang-python method-deep-learning role-framework entity-small-molecule interface-api status-published status-packaged-pypi scope-focused method-physics domain-molecular-simulation entity-trajectory interface-gpu task-md-engine task-ml-potential

Updated Apr 21, 2026
Python

Scindices / BradyAJohnston--MolecularNodes

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

status-active lang-python task-visualization role-plugin domain-structural-biology method-chemoinformatics entity-protein entity-small-molecule scope-focused domain-molecular-simulation entity-trajectory interface-gui role-viewer

Updated Jul 29, 2026
Python

Scindices / glotzerlab--freud

Powerful, efficient particle trajectory analysis in scientific Python.

status-active role-library lang-python lang-cpp task-structure-analysis interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory entity-crystal domain-materials

Updated Jul 29, 2026
C++

Scindices / openmm--openmm-torch

OpenMM plugin to define forces with neural networks

status-active lang-python lang-cpp method-deep-learning role-plugin entity-protein entity-small-molecule interface-api status-published status-packaged-conda scope-focused method-physics domain-molecular-simulation entity-trajectory interface-gpu ecosystem-openmm task-md-engine task-ml-potential

Updated Jun 24, 2026
C++

Scindices / jax-md--jax-md

Differentiable, Hardware Accelerated, Molecular Dynamics

status-active lang-python method-deep-learning role-framework entity-small-molecule interface-api status-published status-packaged-pypi scope-focused method-physics domain-molecular-simulation entity-trajectory interface-gpu entity-crystal task-md-engine task-ml-potential

Updated Jul 26, 2026
Jupyter Notebook

Scindices / nglviewer--ngl

WebGL protein viewer

status-active lang-typescript lang-javascript interface-web task-visualization domain-structural-biology method-chemoinformatics entity-protein entity-small-molecule interface-api status-published scope-focused entity-trajectory role-viewer status-packaged-npm

Updated Apr 14, 2025
TypeScript

Scindices / msmbuilder--msmbuilder

🏗️ Statistical models for biomolecular dynamics 🏗️

lang-python status-archived entity-protein interface-api status-published status-packaged-conda scope-focused method-machine-learning method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory role-toolkit

Updated Jan 26, 2021
Python

Scindices / MDAnalysis--mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

status-active lang-python task-file-io task-structure-analysis entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory role-toolkit ecosystem-mdanalysis scope-swissknife

Updated Jul 23, 2026
Python

Scindices / mdtraj--mdtraj

An open library for the analysis of molecular dynamics trajectories

status-active lang-python lang-c task-file-io task-structure-analysis entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory role-toolkit scope-swissknife

Updated Jul 29, 2026
Python

Scindices / markovmodel--PyEMMA

🚂 Python API for Emma's Markov Model Algorithms 🚂

lang-python status-archived entity-protein interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-machine-learning method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory role-toolkit

Updated Sep 11, 2023
Python

Scindices / molstar--molstar

A comprehensive macromolecular library

status-active lang-typescript lang-javascript interface-web task-visualization domain-structural-biology method-chemoinformatics entity-protein entity-small-molecule interface-api status-published scope-focused entity-complex entity-trajectory role-viewer status-packaged-npm

Updated Jul 29, 2026
TypeScript

Scindices / choderalab--openmmtools

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

status-active role-library lang-python entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-physics method-statistics domain-molecular-simulation entity-trajectory ecosystem-openmm task-md-engine task-free-energy

Updated Jan 7, 2026
Python

Scindices / nglviewer--nglview

Jupyter widget to interactively view molecular structures and trajectories

status-active lang-python lang-javascript interface-web task-visualization role-plugin domain-structural-biology method-chemoinformatics entity-protein entity-small-molecule interface-jupyter status-published status-packaged-pypi status-packaged-conda scope-focused domain-molecular-simulation entity-trajectory role-viewer

Updated Feb 2, 2026
Jupyter Notebook

Scindices / gromacs--gromacs

Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.

status-active lang-cpp interface-cli role-framework entity-protein entity-small-molecule interface-api status-published status-packaged-conda scope-focused method-physics domain-molecular-simulation entity-trajectory interface-gpu lang-cuda task-md-engine

Updated Jul 29, 2026
C++

Scindices / Amber-MD--pytraj

Python interface of cpptraj

status-active role-library lang-python lang-cpp task-file-io entity-protein interface-api status-published status-packaged-conda scope-focused method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory

Updated Mar 6, 2026
Jupyter Notebook

Scindices / deepmodeling--deepmd-kit

A deep learning package for many-body potential energy representation and molecular dynamics

Updated Jul 29, 2026
Python

Scindices / plumed--plumed2

Development version of plumed 2

status-active lang-python lang-cpp interface-cli role-plugin entity-protein entity-small-molecule interface-api status-published status-packaged-conda scope-focused method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory task-free-energy

Updated Jul 20, 2026
C++

Scindices / choderalab--pymbar

Python implementation of the multistate Bennett acceptance ratio (MBAR)

status-active role-library lang-python interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-statistics domain-molecular-simulation entity-trajectory task-free-energy

Updated Feb 12, 2026
Python

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