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.)
☆24Jun 8, 2024Updated last year
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
Sorting:
- Robust and stable clustering of molecular dynamics simulation trajectories.☆19Sep 2, 2022Updated 3 years ago
- Cryptic pocket prediction using AlphaFold 2☆24Nov 27, 2022Updated 3 years ago
- PyEMMA Jupyter Notebooks☆14Jan 28, 2021Updated 5 years ago
- Various scripts for quantum chemistry (mainly ORCA)☆15Feb 6, 2025Updated last year
- QM/MM Study Group☆15Jan 22, 2019Updated 7 years ago
- Computation of the drug-target relative residence times from RAMD simulations☆21Aug 29, 2024Updated last year
- Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.☆16Updated this week
- A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling metho…☆22Sep 26, 2024Updated last year
- ASH is a Python-based computational chemistry and QM/MM environment, primarily for molecular calculations in the gas phase, explicit sol…☆101Updated this week
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆30Jan 23, 2024Updated 2 years ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆48Feb 11, 2021Updated 5 years ago
- Perform polymerization and crosslinking in MARTINI coarse-grained forcefield using GROMACS MD package☆26Jan 21, 2026Updated last month
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆19Updated this week
- Adaptive string method implementation in AmberTools23 and Amber22☆14Jan 7, 2025Updated last year
- For the purpose of post progressing of MD carried by gromacs☆23Jul 2, 2025Updated 8 months ago
- Entropy from PDB conformational ensembles☆13Mar 28, 2024Updated last year
- The official GitHub repository for the Nature Communications paper "Computational Design of Generalist Cyclopropanases with Stereodiverge…☆13Jan 23, 2026Updated last month
- Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface☆42Jan 29, 2026Updated last month
- 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
- Tutorials on doing AMBER based Metadynamics and Gaussian Accelerated MD (GaMD)☆11Dec 1, 2025Updated 3 months ago
- ☆11Oct 23, 2025Updated 4 months ago
- Xlink is a Python script that uses Gromacs to automatically perfom simulation crosslinking and generate atomistic model of aromatic polya…☆16Jul 8, 2023Updated 2 years ago
- Example files for Colvars module: https://github.com/Colvars/colvars☆13Dec 7, 2021Updated 4 years ago
- Snippets for common computer-aided drug design tasks☆10Oct 17, 2017Updated 8 years ago
- Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)☆14Jan 2, 2026Updated 2 months ago
- A unified and modular interface to homology modelling software☆12Sep 27, 2023Updated 2 years ago
- ☆31Jan 26, 2026Updated last month
- An efficient, multithreaded weighted histogram analysis (WHAM) implementation for the post-processing of umbrella MD simulations.☆28Apr 1, 2024Updated last year
- User Guide for MDAnalysis☆29Updated this week
- Software for automated processing of alchemical free energy calculations☆11Nov 7, 2022Updated 3 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
- example demonstrating a free energy estimation starting from OFF and OpenMM☆12Oct 21, 2020Updated 5 years ago
- Generate Ramachandran plots for single PDB structure and as heatmap for MD trajectory☆11Apr 6, 2022Updated 3 years ago
- Pras Server is a library to repair PDB or mmCIF structures, add missing heavy atoms and hydrogen atoms and assign secondary structure by …☆28Aug 10, 2025Updated 6 months ago
- Density based object completion over PBC.☆30Dec 10, 2024Updated last year
- Correlation-based feature selection of Molecular Dynamics simulations☆29Nov 25, 2025Updated 3 months ago
- A tutorials suite for BioSimSpace.☆34Oct 22, 2025Updated 4 months ago
- A python script to prepare GROMACS input files using INTERFACE forcefield☆27Mar 22, 2022Updated 3 years ago
- Demo of diffusion models #DDPM applied to molecular dynamics of small peptide☆14Jan 26, 2024Updated 2 years ago