An open library for the analysis of molecular dynamics trajectories
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Jun 9, 2026 - Python
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mdtraj
Here are 13 public repositories matching this topic...
a python package for the interfacial analysis of molecular simulations
python molecular-dynamics openmm scientific-computing data-analysis lammps charmm simulations molecular-simulations namd gromacs interfaces mdanalysis mdtraj willard-chandler interfacial-atoms sasa
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Jun 11, 2026 - Python
User friendly molecular dynamics simulation combining Modeller, OpenMM and Google Colab: A complete guide
python cheminformatics simulation protein-structure protein gromacs mdanalysis mdtraj ligand colab-tutorial
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Jun 7, 2026 - Python
Tools for Munging Folding@Home datasets
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Sep 20, 2021 - Python
Modular Python toolkit for running OpenMM molecular dynamics simulations and automated trajectory analysis (RMSD, PCA, FEL, DSSP, H-bonds, SASA, contact maps)
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Jun 4, 2026 - Python
Molecular Dynamics - Simulation Analysis and Preparation Suite
python science molecular-dynamics python3 gromacs amber biophysics mdanalysis mdtraj metadynamics plumed2
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Feb 4, 2025 - Python
Auxiliary tools and scripts initially made for my PhD projects.
python bash science hpc jupyter-notebook molecular-dynamics slurm biophysics mdanalysis mdtraj metadynamics plumed2
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Jul 7, 2025 - Jupyter Notebook
Molecular dynamics pre- and post-processing toolkit.
python cheminformatics clustering structural-biology molecular-dynamics pytorch openmm computational-chemistry pca tica rdkit numba free-energy gromacs trajectory-analysis mdtraj cupy jax md-analysis openfe
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Jun 5, 2026 - Python
Google colab notebooks for typical MD trajectory analysis routines with Python
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Sep 27, 2024 - Jupyter Notebook
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Jun 22, 2018 - Jupyter Notebook
Analysis of RoseTTAFold2NA and AlphaFold 3 structure predictions to understand whether it can be used to determine the spacing and/or orientation preferences of transcription factors
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Feb 10, 2025 - Python
A published paper in PEARC18: Combining HPC and Big Data Infrastructures in Large-Scale Post-Processing of SimulaBon Data: A Case Study
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Jul 23, 2018 - Python
Implementation of MDTraj in Rust
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Mar 27, 2026 - Rust
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