Collection of Python scripts to setup and run simulations with OpenMM
☆17May 22, 2020Updated 5 years ago
Alternatives and similar repositories for openmm_scripts
Users that are interested in openmm_scripts are comparing it to the libraries listed below
Sorting:
- An open-source library for the analysis of protein interactions.☆33Dec 5, 2021Updated 4 years ago
- A collections of scripts for working molecular dynamics simulations☆45Feb 6, 2026Updated last month
- Source code for "Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome inter…☆13Jun 17, 2022Updated 3 years ago
- Optimization tool for calibrating coarse-grained force fields of lipids, relying on the simultaneous usage of reference AA trajectories (…☆10Jun 6, 2023Updated 2 years ago
- Implementation of MOFF force field. Please cite us at Latham, A; Zhang, B J. Chem. Theory Comput. 2021, 17, 3134. (https://pubs.acs.org/d…☆10Jun 16, 2022Updated 3 years ago
- ☆48Mar 5, 2026Updated 2 weeks ago
- Algorithm for identifying hydrogen bond networks in CG proteins to implement Go-like Martini 3 models☆16Oct 25, 2024Updated last year
- 👑 A lightweight molecular dynamics pipeline for running protein simulations on portable hardware☆31Feb 9, 2026Updated last month
- Repository for MD methods and analysis from submitted or published work☆20Jun 10, 2023Updated 2 years ago
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆28May 2, 2020Updated 5 years ago
- Set of Python scripts designed to be a dependency-free cross-platform swiss army knife for PDB files.☆26Jun 23, 2022Updated 3 years ago
- Google Colaboratory Notebooks for Computational Biochemistry☆21Jun 15, 2025Updated 9 months ago
- example demonstrating a free energy estimation starting from OFF and OpenMM☆12Oct 21, 2020Updated 5 years ago
- Display PackedPose objects, Pose objects, or PDB files within a Jupyter notebook and Google Colab☆11Oct 16, 2022Updated 3 years ago
- Modeling molecular ensembles with scalable data structures and parallel computing☆37Mar 11, 2026Updated last week
- Some Rosetta Scripts that allow for various simple tasks☆15Jan 27, 2020Updated 6 years ago
- a library for massive analyses of internal voids in biomolecules and ligand transport through them☆10Mar 10, 2026Updated last week
- Contact map analysis for biomolecules; based on MDTraj☆48Jan 25, 2026Updated last month
- A command line application to launch molecular dynamics simulations with OpenMM☆40Apr 7, 2022Updated 3 years ago
- Rapid Generation of Rare Event Pathways Using Direction Guided Adaptive Sampling: From Ligand Unbinding to Protein (Un)Folding☆38Nov 25, 2025Updated 3 months ago
- Learn molecular simulation with Python☆17Dec 31, 2024Updated last year
- A mobile QML app for interfacing with the Galaxy API☆14Dec 7, 2015Updated 10 years ago
- Protocols for running MD simulations in Gromacs☆10Jun 18, 2024Updated last year
- Protein-Protein Docking using Genetic Algorithm☆20Mar 9, 2026Updated last week
- References, presentations and other resources☆15Oct 31, 2023Updated 2 years ago
- Synthetic mzML writer☆13Mar 10, 2025Updated last year
- Fraction of Common Contacts Clustering Algorithm for Protein Structures☆27Aug 12, 2021Updated 4 years ago
- ☆70Jul 19, 2023Updated 2 years ago
- A python toolkit for analysing membrane protein-lipid interactions.☆70Oct 22, 2025Updated 5 months ago
- ☆72Feb 24, 2026Updated 3 weeks ago
- ☆70Feb 13, 2026Updated last month
- Plugin for folding sequences directly in PyMOL☆28Aug 5, 2025Updated 7 months ago
- A Generalised workflow for obtaining protein and peptide molecular structures, docking the peptide into the protein and running a molecul…☆15Jan 1, 2025Updated last year
- Various tutorials about MD setup and analysis, protein-ligand docking, machine learning and lots of other interesting things.☆35Jan 2, 2021Updated 5 years ago
- MD DaVis: A python package to analyze molecular dynamics trajectories of proteins☆17Feb 17, 2025Updated last year
- Ligand-Receptor docking with AutoDock Vina☆12Mar 21, 2024Updated 2 years ago
- Various integrations to the Schrodinger ecosystem. With major interest on analysis tools for Molecular Dynamics simulations run with Desm…☆23Mar 3, 2026Updated 2 weeks ago
- Slides + Iframe = sliFrame☆55Apr 6, 2025Updated 11 months ago
- Dock Multiple Ligands with AutoDock Vina with one Command☆11Jan 10, 2018Updated 8 years ago