giribio / MDNotebooksLinks
Jupyter Notebooks for Molecular Dynamics
☆41Updated 3 years ago
Alternatives and similar repositories for MDNotebooks
Users that are interested in MDNotebooks are comparing it to the libraries listed below
Sorting:
- Analysis of non-covalent interactions in MD trajectories☆57Updated 5 months ago
- ☆65Updated last year
- A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories…☆29Updated last year
- ☆28Updated last month
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆34Updated last year
- Yasara plugins for Gromacs users☆27Updated last year
- Input files for GROMACS tutorials written for the Journal of Physical Chemistry B☆19Updated 10 months ago
- The pDynamo molecular modeling and simulation program☆37Updated 3 weeks ago
- Trusted force field files for gromacs☆50Updated 7 months ago
- Package for storage and analysis of virtual screenings run with AutoDock-GPU and AutoDock Vina☆48Updated 2 weeks ago
- Random Acceleration Molecular Dynamics in GROMACS☆37Updated 10 months ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆44Updated 4 years ago
- MD pharmacophores and virtual screening☆33Updated 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…☆23Updated 11 months ago
- a VMD plugin for binding affinity prediction using end-point free energy methods☆28Updated 9 years ago
- A collections of scripts for working molecular dynamics simulations☆43Updated last year
- Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface☆35Updated 3 years ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆69Updated 4 months ago
- Molecular Dynamics for Experimentalists☆57Updated this week
- ☆54Updated 2 years ago
- (Linux and macOS) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina☆69Updated last year
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆60Updated last year
- End-to-end ML workflow based on the talk I gave in CHE596.☆11Updated 10 months ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆16Updated 2 years ago
- Contact map analysis for biomolecules; based on MDTraj☆45Updated 5 months ago
- MMTSB Tool Set☆31Updated 2 weeks ago
- Automatic gromacs protocol from preparation to production with ligand parametrization through☆68Updated 2 months ago
- Collection of Python scripts to setup and run simulations with OpenMM☆17Updated 5 years ago
- ☆40Updated 2 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated 2 years ago