Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.
☆24Oct 18, 2019Updated 6 years ago
Alternatives and similar repositories for cp2K_qmmm_tutorials_for_biological_simulations
Users that are interested in cp2K_qmmm_tutorials_for_biological_simulations are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface☆43Jan 29, 2026Updated 3 months ago
- The official GitHub repository for the Nature Communications paper "Computational Design of Generalist Cyclopropanases with Stereodiverge…☆13Jan 23, 2026Updated 3 months ago
- A repository containing the build steps for the ccpbiosim workshop on QM/MM☆68Updated this week
- A tutorials suite for BioSimSpace.☆37Oct 22, 2025Updated 6 months ago
- Adaptive string method implementation in AmberTools23 and Amber22☆15Jan 7, 2025Updated last year
- AI Agents on 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.
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆41Apr 27, 2026Updated last week
- A python script to perform QM/MM calculation.☆13Apr 29, 2026Updated last week
- QM/MM Study Group☆15Jan 22, 2019Updated 7 years ago
- Academic license pre-required. While FEP Plus charge you 100,000 USD per year. Here comes the FEP-Minus, it is a Schrodinger FEP Plus ide…☆25Jul 28, 2024Updated last year
- Generate Ramachandran plots for single PDB structure and as heatmap for MD trajectory☆11Apr 6, 2022Updated 4 years ago
- Different run and analysis scripts as described in the research guides.☆14Jul 5, 2022Updated 3 years ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆68Apr 16, 2021Updated 5 years ago
- For the purpose of post progressing of MD carried by gromacs☆23Jul 2, 2025Updated 10 months ago
- Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems☆15Jun 15, 2019Updated 6 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- NAMD QM/MM Tutorial on Free Energy Profile of Reaction Mechanisms☆15Sep 14, 2018Updated 7 years ago
- Robust and stable clustering of molecular dynamics simulation trajectories.☆19Sep 2, 2022Updated 3 years ago
- ☆25Aug 1, 2023Updated 2 years ago
- Automated construction of protein chimeras and their analysis.☆14Sep 29, 2023Updated 2 years ago
- A Python library for constructing polymer topologies and coordinates☆21Sep 23, 2025Updated 7 months ago
- ☆11Sep 16, 2024Updated last year
- ☆33Sep 23, 2023Updated 2 years ago
- ☆15Jun 26, 2018Updated 7 years ago
- This software package simulates the reduction of graphene oxide and calculates the optical response of the generated sp2 domains☆11Dec 22, 2016Updated 9 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.
- Supernova's MM-PBSA binding free energy calculation tool.☆12Apr 28, 2026Updated last week
- ASH is a Python-based computational chemistry and QM/MM environment, primarily for molecular calculations in the gas phase, explicit sol…☆113Apr 28, 2026Updated last week
- ☆40Jul 17, 2024Updated last year
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆25Jun 8, 2024Updated last year
- OMNI-P2x: A universal neural network potential for excited states☆13Mar 19, 2026Updated last month
- EnzyHTP is a python library that automates the complete life-cycle of enzyme modeling☆35Updated this week
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆210Sep 22, 2023Updated 2 years ago
- Example files for Colvars module: https://github.com/Colvars/colvars☆13Dec 7, 2021Updated 4 years ago
- Perform polymerization and crosslinking in MARTINI coarse-grained forcefield using GROMACS MD package☆29Jan 21, 2026Updated 3 months ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- Entropy from PDB conformational ensembles☆13Mar 28, 2024Updated 2 years ago
- Learning free energy landscapes using artificial neural networks☆14Nov 30, 2017Updated 8 years ago
- a Python program for running QM/MM simulations using Q-Chem and OpenMM☆16Apr 24, 2022Updated 4 years ago
- code and source data for de novo design of Kemp elimination paper☆25Sep 18, 2025Updated 7 months ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆19Apr 23, 2026Updated last week
- A python implementation of pdb2oniom for QM/MM (ONIOM) calculations☆11Oct 2, 2025Updated 7 months ago
- METIS: A versatile active learning workflow for optimization of genetic and metabolic networks☆35Nov 7, 2022Updated 3 years ago