Example files for Colvars module: https://github.com/Colvars/colvars
☆14Dec 7, 2021Updated 4 years ago
Alternatives and similar repositories for examples
Users that are interested in examples 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
- Fast PBC wrapping and unwrapping for VMD☆27Nov 25, 2024Updated last year
- Collective variables library for molecular simulation and analysis programs☆241Aug 2, 2026Updated last week
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆43Apr 27, 2026Updated 3 months ago
- The gmx_rrcs script is designed to calculate the residues-residues contact scores (rrcs) from a trajectory file generated by GROMACS.☆18Jun 16, 2025Updated last year
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Main repository for METAGUI3☆22Jun 19, 2021Updated 5 years ago
- ☆11Oct 18, 2019Updated 6 years ago
- Tools for coarse-grained molecular dynamics simulations using the SPICA force field☆13May 12, 2026Updated 2 months ago
- Convenience functions for VMD-TCL scripting☆14Apr 3, 2026Updated 4 months ago
- Main code repository for FATSLiM☆23Feb 13, 2022Updated 4 years ago
- Calculate position-dependent diffusivity functions from trajectory data (usually from molecular dynamics). The approach is described in h…☆11Mar 25, 2025Updated last year
- binding free energy estimator 2☆146Jul 29, 2026Updated last week
- An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics☆18Sep 11, 2022Updated 3 years ago
- Adaptive sampling algorithms for molecular transitions☆29Jun 28, 2026Updated last month
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Learning free energy landscapes using artificial neural networks☆15Nov 30, 2017Updated 8 years ago
- Python Tools for NAMD☆24May 7, 2025Updated last year
- Spectral Gap Optimization of Parameters☆18Mar 28, 2020Updated 6 years ago
- Tutorials on doing AMBER based Metadynamics and Gaussian Accelerated MD (GaMD)☆13Dec 1, 2025Updated 8 months ago
- A deep learning-based framework to uniquely identify an uncorrelated, isometric and meaningful latent representation.☆19Sep 12, 2023Updated 2 years ago
- Daily analyses of genomic SARS-CoV-2 data☆15Nov 8, 2022Updated 3 years ago
- Automatic Mutual Information Noise Omission☆16Oct 8, 2024Updated last year
- Collection of interaction and molecule parameters for the Martini3 force-field☆22Feb 7, 2023Updated 3 years ago
- python simulation interface for molecular modeling. To cite this software publication: https://www.sciencedirect.com/science/article/pii/…☆13Aug 24, 2016Updated 9 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- A library of optimized math functions targeted at 32-bit and 64-bit x86 Linux systems☆30Apr 11, 2016Updated 10 years ago
- Axel Kohlmeyer's development repository of the LAMMPS MD software package☆12Updated this week
- ☆12Jul 30, 2019Updated 7 years ago
- A collection of tools for DNA modelling☆25Jun 4, 2026Updated 2 months ago
- PyEMMA Jupyter Notebooks☆13Jan 28, 2021Updated 5 years ago
- Tutorial for the usage of the dcTMD approach and Langevin simulations employing the trypsin-benzamidine complex as example.☆11Jul 15, 2024Updated 2 years ago
- Repository of the data for PLUMED Masterclass 22.3☆15Jul 10, 2024Updated 2 years ago
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆28Jun 8, 2024Updated 2 years ago
- Accelerating Metadynamics-Based Free-Energy Calculations with Adaptive Machine Learning Potentials☆18Jun 9, 2021Updated 5 years ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Molecular dynamics workflow framework in python.☆12Nov 15, 2022Updated 3 years ago
- Set of tools to generate a multi-eGO force field to perform molecular dynamics simulations☆16Aug 3, 2026Updated last week
- PiViewer: an open-source tool for automated detection and display of pi-pi interactions☆14Jun 6, 2018Updated 8 years ago
- ☆18Jan 15, 2026Updated 6 months ago
- C++ Accelerated Python Diffusion Maps Library☆24Aug 28, 2018Updated 7 years ago
- Comparison of principal components analysis with diffusion maps on toy data sets and a molecular simulation trajectory☆17Feb 1, 2017Updated 9 years ago
- Some useful VMD scrpits☆10May 24, 2016Updated 10 years ago