MobleyLab / basic_simulation_training
A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations (oriented towards molecular dynamics (MD)), providing some training itself and linking out to other helpful information elsewhere. The intent is that this provide information on the prerequisites which will be …
☆114Updated 6 years ago
Alternatives and similar repositories for basic_simulation_training:
Users that are interested in basic_simulation_training are comparing it to the libraries listed below
- Experimental and calculated small molecule hydration free energies☆116Updated 2 years ago
- Force fields produced by the Open Force Field Initiative☆148Updated last month
- Martini 3 small-molecule database☆58Updated 7 months ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆141Updated 3 months ago
- CAlculation of NMR Chemical Shifts using Deep LEarning☆58Updated 2 years ago
- psi4+RDKit☆99Updated 2 years ago
- LOOS: a lightweight object-oriented structure analysis library☆124Updated last month
- High level API for using machine learning models in OpenMM simulations☆100Updated 2 weeks ago
- Describe and apply transformation on molecular structures and topologies☆108Updated this week
- Quantum Mechanical Bespoke Force Field Derivation Toolkit☆97Updated 8 months ago
- Best Practices article intended for LiveCoMS☆39Updated 5 years ago
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆43Updated 3 years ago
- the simple alchemistry library☆210Updated 3 months ago
- OpenMM plugin to interface with PLUMED☆66Updated last month
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆183Updated last year
- ☆64Updated last year
- ☆53Updated last year
- ☆91Updated 3 years ago
- An open tool implementing some recommended practices for analyzing alchemical free energy calculations☆126Updated 10 months ago
- 📐 Symmetry-corrected RMSD in Python☆93Updated 4 months ago
- LiveCoMS GROMACS Tutorials Paper☆113Updated 5 years ago
- Automatic MARTINI parametrization of small organic molecules☆66Updated 4 months ago
- Enable cheminformatics and quantum chemistry☆72Updated last year
- ☆123Updated 11 months ago
- An Open-Source Molecular Builder and Free Energy Preparation Workflow☆122Updated 2 weeks ago
- Physical validation of molecular simulations☆56Updated 2 months ago
- A python toolkit for analysing membrane protein-lipid interactions.☆63Updated last year
- Sire Molecular Simulations Framework☆95Updated last year
- A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.☆66Updated last year
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆78Updated 9 months ago