MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshell) and the ORCA code as QM code for Chemshell.)
☆28Jun 8, 2024Updated 2 years ago
Alternatives and similar repositories for chemshell-QMMM-protein-setup
Users that are interested in chemshell-QMMM-protein-setup are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Various scripts for quantum chemistry (mainly ORCA)☆15Feb 6, 2025Updated last year
- Cryptic pocket prediction using AlphaFold 2☆25Nov 27, 2022Updated 3 years ago
- QM/MM Study Group☆15Jan 22, 2019Updated 7 years ago
- Robust and stable clustering of molecular dynamics simulation trajectories.☆20Sep 2, 2022Updated 3 years ago
- Combines FRESEAN mode analysis of a protein (based on a CG representation) with enhanced sampling using metadynamics☆16May 7, 2026Updated 2 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆48Feb 11, 2021Updated 5 years ago
- PyEMMA Jupyter Notebooks☆13Jan 28, 2021Updated 5 years ago
- This repository contained python code used to do organic free energy calculation. Reference: http://www.bevanlab.biochem.vt.edu/Pages/Per…☆11Aug 2, 2018Updated 7 years ago
- The App Store for VMD extensions.☆14Jan 14, 2023Updated 3 years ago
- NAMD QM/MM Tutorial on Free Energy Profile of Reaction Mechanisms☆16Sep 14, 2018Updated 7 years ago
- ☆18Jan 15, 2026Updated 6 months ago
- A collection of scripts which I have developed to use GROMACS, for both compute clusters and post-simulation analysis.☆11Jul 15, 2014Updated 12 years ago
- ASH is a Python-based computational chemistry and QM/MM environment, primarily for molecular calculations in the gas phase, explicit sol…☆120Updated this week
- Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.☆17Jul 13, 2026Updated last week
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆30Jan 23, 2024Updated 2 years ago
- An efficient, multithreaded weighted histogram analysis (WHAM) implementation for the post-processing of umbrella MD simulations.☆29Apr 1, 2024Updated 2 years ago
- Improving protein–ligand docking and screening accuracies by incorporating a scoring function correction term☆32Dec 2, 2024Updated last year
- Adaptive string method implementation in AmberTools23 and Amber22☆15Jan 7, 2025Updated last year
- A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling metho…☆24Sep 26, 2024Updated last year
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆19Apr 16, 2026Updated 3 months ago
- A python implementation of the string method with swarms of trajectories using GROMACS☆19Oct 19, 2022Updated 3 years ago
- Computation of the drug-target relative residence times from RAMD simulations☆23Aug 29, 2024Updated last year
- Software for automated processing of alchemical free energy calculations☆12Nov 7, 2022Updated 3 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.
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆16Apr 16, 2025Updated last year
- Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface☆43Jan 29, 2026Updated 5 months ago
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆26Oct 18, 2019Updated 6 years ago
- Resources for Learning Cheminformatics with the RDKit☆19Apr 7, 2019Updated 7 years ago
- Entropy from PDB conformational ensembles☆13Mar 28, 2024Updated 2 years ago
- Example files for Colvars module: https://github.com/Colvars/colvars☆14Dec 7, 2021Updated 4 years ago
- ☆20Jun 14, 2026Updated last month
- Learning free energy landscapes using artificial neural networks☆15Nov 30, 2017Updated 8 years ago
- ☆31Jul 8, 2026Updated last week
- 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.
- Machine Learning based toxicity prediction tool for small molecules.☆11Feb 13, 2024Updated 2 years ago
- Demo of diffusion models #DDPM applied to molecular dynamics of small peptide☆14Jan 26, 2024Updated 2 years ago
- For the purpose of post progressing of MD carried by gromacs☆24Jul 2, 2025Updated last year
- Perform polymerization and crosslinking in MARTINI coarse-grained forcefield using GROMACS MD package☆30Jan 21, 2026Updated 6 months ago
- The official GitHub repository for the Nature Communications paper "Computational Design of Generalist Cyclopropanases with Stereodiverge…☆15Jan 23, 2026Updated 5 months ago
- Density based object completion over PBC.☆33Apr 23, 2026Updated 2 months ago
- An implementation of the Solubility Forecast Index (SFI)☆25Oct 6, 2025Updated 9 months ago