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mdtraj

Here are 10 public repositories matching this topic...

mdtraj / mdtraj

An open library for the analysis of molecular dynamics trajectories

python pdb molecular-dynamics dihedral-angles mdtraj rmsd pdb-files molecular-dynamics-trajectories

Updated Nov 19, 2024
Python

Marcello-Sega / pytim

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

Updated Nov 4, 2024
Python

paulshamrat / ColabMDA

User friendly molecular dynamics simulation combining GROMACS and Google Colab: A complete guide

python cheminformatics protein-structure gromacs mdanalysis mdtraj colab-tutorial

Updated Sep 15, 2024
Jupyter Notebook

choderalab / fahmunge

Tools for Munging Folding@Home datasets

python pipeline mdtraj foldingathome fah

Updated Sep 20, 2021
Python

ravenswing / mdsaps

Molecular Dynamics - Simulation Analysis and Preparation Suite

python science molecular-dynamics python3 gromacs amber biophysics mdanalysis mdtraj metadynamics plumed2

Updated Sep 4, 2024
Python

ravenswing / phd_tools

Auxiliary tools and scripts initially made for my PhD projects.

python bash science hpc jupyter-notebook molecular-dynamics slurm biophysics mdanalysis mdtraj metadynamics plumed2

Updated Oct 9, 2024
Jupyter Notebook

matsunagalab / tutorial_analyzingMDdata

Google colab notebooks for typical MD trajectory analysis routines with Python

tutorial scikit-learn molecular-dynamics mdtraj

Updated Sep 27, 2024
Jupyter Notebook

ShuklaGroup / optimalProbes

https://github.com/ShuklaGroup/optimalProbes/wiki

genetic-algorithm msmbuilder deer mdtraj optimalprobes optimal-probes

Updated Jun 22, 2018
Jupyter Notebook

gilga001 / HPCandBigDataPipeline

A published paper in PEARC18: Combining HPC and Big Data Infrastructures in Large-Scale Post-Processing of SimulaBon Data: A Case Study

python simulation hpc bigdata mdtraj postprocessing apachespark

Updated Jul 23, 2018
Python

i-l-sokolov / RosettaFoldNA_output_analysis

Analysis of RoseTTAFold2NA structure predictions to understand whether it can be used to determine the spacing and/or orientation preferences of transcription factors

python protein-structure mdtraj rosettafold dna-structure

Updated Jun 30, 2024
Python

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