scripts for analyzing molecular dynamics trajectories using VMD
☆40May 28, 2015Updated 11 years ago
Alternatives and similar repositories for md-analysis-tools
Users that are interested in md-analysis-tools are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Generate Ramachandran plots for single PDB structure and as heatmap for MD trajectory☆11Apr 6, 2022Updated 4 years ago
- Some of useful tcl scripts to analyse data from VMD☆16Aug 2, 2022Updated 4 years ago
- Analysis of non-covalent interactions in MD trajectories☆72Jan 3, 2025Updated last year
- ☆12Dec 19, 2016Updated 9 years ago
- a VMD plugin for binding affinity prediction using end-point free energy methods☆30Apr 23, 2016Updated 10 years ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Tutorials and examples for nicer animations (movies) and images in PyMOL.☆21Oct 6, 2026Updated 3 weeks ago
- A set of python scripts for automating iterative the iterative Boltzmann inversion method using LAMMPS.☆14Jun 10, 2015Updated 11 years ago
- analyze 1D (e)ABF simulation in NAMD☆11Nov 12, 2018Updated 7 years ago
- Robust and stable clustering of molecular dynamics simulation trajectories.☆20Sep 2, 2022Updated 4 years ago
- Example files for Colvars module: https://github.com/Colvars/colvars☆14Dec 7, 2021Updated 4 years ago
- Python Tools for NAMD☆25May 7, 2025Updated last year
- Jupyter Notebook showing how to plot FES, histograms and time-series data using Matplotlib.☆13Dec 21, 2020Updated 5 years ago
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆16Jan 20, 2022Updated 4 years ago
- Generate coarse-grained molecular dynamics models from atomistic trajectories.☆69Aug 2, 2026Updated 3 months ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- A VMD script to calculate side-chain and backbone dihedrals (torsion angles)☆14Jun 4, 2016Updated 10 years ago
- A collection of scripts which I have developed to use GROMACS, for both compute clusters and post-simulation analysis.☆12Jul 15, 2014Updated 12 years ago
- Master project repository for Gøran Brekke Svaland. Molecular Dynamics using LAMMPS. CLAYFF. REAXFF.☆12May 26, 2015Updated 11 years ago
- Modify Gromcas enabling CIF file supporting☆11Sep 8, 2023Updated 3 years ago
- Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.☆15Sep 20, 2018Updated 8 years ago
- ☆32Jul 8, 2026Updated 3 months ago
- Materials, issues and things for the 2018 Workshop and Hackathon☆15Jul 25, 2025Updated last year
- Cryptic pocket prediction using AlphaFold 2☆25Nov 27, 2022Updated 3 years ago
- Count rings in a undirected graph.☆18May 6, 2023Updated 3 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Cloud GPU supported NAMD3-based binding free energy difference between two small molecules against the same protein target. This is prob…☆28Oct 21, 2026Updated last week
- Tools for computing spectral heat current distribution using LAMMPS NEMD simulations.☆15Mar 11, 2020Updated 6 years ago
- a logistics and persistence engine for the analysis of molecular dynamics trajectories☆30Jan 24, 2020Updated 6 years ago
- 厦门大学疫情自动打卡☆12Dec 9, 2022Updated 3 years ago
- ProLint 2.0: a scalable framework for the analysis of biomolecular interactions in MD simulations.☆12Jun 14, 2026Updated 4 months ago
- Notebooks for NYU Statistical Mechanics☆20Jul 6, 2023Updated 3 years ago
- Coarse-graining library that implements Force-matching☆11Aug 31, 2020Updated 6 years ago
- A Python workflow to study protein-protein coevolution and interaction☆21Jun 30, 2017Updated 9 years ago
- Generates Martini models for open carbon nanotubes to use with Gromacs.☆15Nov 24, 2021Updated 4 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- MDToolbox: A MATLAB/Octave toolbox for statistical analysis of molecular dynamics trajectories☆27Dec 7, 2019Updated 6 years ago
- A novel approach to pose selection in protein-ligand docking based on graph theory.☆20Nov 22, 2016Updated 9 years ago
- This repo contains the codes to run solvation free energy prediction.☆13May 1, 2022Updated 4 years ago
- clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)☆135Apr 25, 2024Updated 2 years ago
- Open Source, Prepare a molecular dynamic simulation from scratch without installing local VMD, use LigParGen for topology, it is one of t…☆14Jul 3, 2023Updated 3 years ago
- Input files and results of paper: Phase equilibrium of liquid water and hexagonal from ice enhanced sampling molecular dynamics simulatio…☆11Apr 9, 2021Updated 5 years ago
- Input files for GROMACS tutorials written for the Journal of Physical Chemistry B☆27Jul 21, 2024Updated 2 years ago