some scripts for analysis of MD and CADD. And some tutorials.
☆61Aug 12, 2024Updated last year
Alternatives and similar repositories for DuIvy
Users that are interested in DuIvy are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A Tool to process and visualize the results of molecular dynamics simulations(GROMACS).☆103Feb 18, 2026Updated last month
- For the purpose of post progressing of MD carried by gromacs☆23Jul 2, 2025Updated 8 months ago
- gromacs(Protein-Ligand Complex)☆11Sep 20, 2022Updated 3 years ago
- Scripts for running alchemical, free-energy perturbation simulations using Gromacs☆17Feb 27, 2018Updated 8 years ago
- Data and script of Umbrella Sampling for molecular transmembrane☆14Jun 21, 2024Updated last year
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- gmx_corr converts the covariance matrix which is produced by GROMACS covar to cross correlation matrix and creates a heat map figure.☆11Oct 11, 2022Updated 3 years ago
- Protocols for running MD simulations in Gromacs☆10Jun 18, 2024Updated last year
- A Python package to generate free energy landscape (FEL) of molecular dynamics (MD) trajectory obtained from GROMACS. It also extracts th…☆14Apr 4, 2025Updated 11 months ago
- tools for GROMACS☆144Jul 11, 2025Updated 8 months ago
- gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.☆300Dec 8, 2025Updated 3 months ago
- Analysis of contacts in molecular dynamics trajectories☆45Nov 4, 2019Updated 6 years ago
- binding free energy estimator 2☆137Updated this week
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆207Sep 22, 2023Updated 2 years ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆46May 3, 2021Updated 4 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- molecular dynamics simulation and analysis. 分子动力学模拟和分析。☆41Oct 3, 2019Updated 6 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…☆24Jun 8, 2024Updated last year
- DISTEVAL: A web-server for evaluating protein inter-residue distances☆18Mar 7, 2022Updated 4 years ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆97Jul 16, 2025Updated 8 months ago
- Gromacs Implementation of OPLS-AAM Force field☆15Aug 5, 2018Updated 7 years ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Jul 28, 2022Updated 3 years ago
- Applying Machine Learning methodologies in search of novel MOF's and battery materials.☆13May 31, 2023Updated 2 years ago
- Source code and input files associated to the paper "Targeted free energy perturbation revisited: Accurate free energies from mapped refe…☆13Sep 14, 2021Updated 4 years ago
- ☆31Mar 11, 2026Updated 2 weeks 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.
- The central entry point to the P2Rank project with links to the individual projects, including references to documentation, datasets, etc…☆13Feb 11, 2026Updated last month
- ☆10Nov 23, 2018Updated 7 years ago
- CHAPERONg: An automated pipeline for GROMACS MD simulations and trajectory analyses☆60Aug 2, 2025Updated 7 months ago
- A collection of scripts which I have developed to use GROMACS, for both compute clusters and post-simulation analysis.☆11Jul 15, 2014Updated 11 years ago
- Random Acceleration Molecular Dynamics in GROMACS☆44Jul 19, 2024Updated last year
- Temperature generator for Replica Exchange MD simulations☆29Dec 14, 2022Updated 3 years ago
- PyPEF – Pythonic Protein Engineering Framework☆25Sep 20, 2025Updated 6 months ago
- ☆15Jun 26, 2018Updated 7 years ago
- implicit or explicit water model based docking with Autodock vina engine. supporting pharmacophore /position constrained docking☆73Feb 9, 2026Updated last month
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆83Jan 8, 2025Updated last year
- ParametrizANI - Fast, Accurate and Free Dihedral Parametrization in the Cloud with TorchANI☆22Jul 28, 2025Updated 7 months ago
- Build coarse-grained mapping for molecules from a web-GUI☆18Sep 10, 2021Updated 4 years ago
- A distance distribution-based visualization method for atomic pair energy and precise prediction of absolute binding free energy.☆15Feb 4, 2025Updated last year
- Automated bonded parameters for Martini 3☆26Jul 20, 2025Updated 8 months ago
- Package for reading, analysis and visualization of metadynamics HILLS☆39Nov 28, 2023Updated 2 years ago
- ☆30May 15, 2025Updated 10 months ago