☆11Oct 18, 2019Updated 6 years ago
Alternatives and similar repositories for ABF-example-files-for-NAMD-and-OpenMM
Users that are interested in ABF-example-files-for-NAMD-and-OpenMM are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- NAMD QM/MM Tutorial on Free Energy Profile of Reaction Mechanisms☆15Sep 14, 2018Updated 7 years ago
- NAMD-xtb-QMMM-interface☆11Jul 21, 2020Updated 5 years ago
- Detect and characterize binding pockets from molecular simulations.☆15Mar 17, 2026Updated last week
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆18Mar 16, 2026Updated last week
- Enhanced sampling methods for molecular dynamics simulations☆43Dec 16, 2022Updated 3 years ago
- DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- VMD plugin to calculate and visualize clusters of conformations for a trajectory☆23Oct 24, 2018Updated 7 years ago
- Example files for Colvars module: https://github.com/Colvars/colvars☆13Dec 7, 2021Updated 4 years ago
- Scripts for PCA and related analyses of lipid motions☆10Jun 21, 2022Updated 3 years ago
- Implementation of corrections for diffusion coefficients in membrane simulations.☆10Aug 2, 2022Updated 3 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☆137Mar 22, 2026Updated last week
- Convenience functions for VMD-TCL scripting☆14Jul 16, 2025Updated 8 months ago
- Building and analyzing residue interaction networks with cofactors (includes tutorial).☆18Mar 31, 2021Updated 4 years ago
- A Python program for QM/MM Simulations based on the Perturbed Matrix Method☆26Oct 17, 2023Updated 2 years ago
- DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Mar 18, 2019Updated 7 years ago
- ☆46Feb 17, 2026Updated last month
- example demonstrating a free energy estimation starting from OFF and OpenMM☆12Oct 21, 2020Updated 5 years ago
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆15Mar 20, 2026Updated last week
- A Python package to compute and analyze transport properties.☆16Jul 27, 2025Updated 8 months ago
- Automatic Mutual Information Noise Omission☆16Oct 8, 2024Updated last year
- Using supervised machine learning to build collective variables for accelerated sampling☆28Jun 26, 2018Updated 7 years ago
- Learn molecular simulation with Python☆17Dec 31, 2024Updated last year
- Spectral Gap Optimization of Parameters☆18Mar 28, 2020Updated 6 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- easyPARM is a computational tool developed to simplify the derivation of force field parameters for metal-containing molecular systems an…☆35Mar 12, 2026Updated 2 weeks ago
- ☆30May 31, 2023Updated 2 years ago
- Rethinking Metadynamics: From Bias Potentials to Probability Distributions☆14Sep 18, 2023Updated 2 years ago
- Statistical models for biomolecular dynamics☆42May 8, 2025Updated 10 months ago
- A GUI program for plotting Minimal energy path on potential energy surface.☆42Jan 18, 2021Updated 5 years ago
- Adaptive sampling algorithms for molecular transitions☆26Mar 19, 2026Updated last week
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆13Mar 7, 2025Updated last year
- The Molecular Modelling Toolkit☆54Apr 11, 2025Updated 11 months ago
- For the purpose of post progressing of MD carried by gromacs☆23Jul 2, 2025Updated 8 months ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆15Jan 3, 2026Updated 2 months ago
- GridDataFormats is a pure Python library to handle data on a regular grid using commonly used file formats in molecular simulations.☆32Jan 23, 2026Updated 2 months ago
- A Python package to improve the accessibility and reproducibility of enhanced sampling simulations☆15May 16, 2018Updated 7 years ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Jan 16, 2015Updated 11 years ago
- ☆27Jan 20, 2022Updated 4 years ago
- A Python Package to Automate Thermodynamic Integration Calculations for Free Energy☆32Mar 16, 2026Updated last week
- Source code for HOLE program.☆39Aug 15, 2024Updated last year