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 …
☆119Dec 29, 2018Updated 7 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. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by…☆165Mar 11, 2025Updated last year
- A python implementation of pdb2oniom for QM/MM (ONIOM) calculations☆12Oct 2, 2025Updated 10 months ago
- ☆126Feb 4, 2026Updated 6 months ago
- Examples of applications of pymbar to various problems in simulation and experiment☆24Jan 16, 2015Updated 11 years ago
- A primer on software development best practices for computational chemistry☆276Dec 5, 2022Updated 3 years ago
- 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.
- Best Practices article intended for LiveCoMS☆43Mar 26, 2026Updated 4 months ago
- Physical validation of molecular simulations☆65Jul 6, 2026Updated last month
- Parameter/topology editor and molecular simulator☆452Jul 1, 2026Updated last month
- Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling☆34Jul 31, 2026Updated last week
- Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.☆15Sep 20, 2018Updated 7 years ago
- How to analyze molecular dynamics data with PyEMMA☆88May 29, 2019Updated 7 years ago
- Analysis of non-covalent interactions in MD trajectories☆70Jan 3, 2025Updated last year
- Quickly generate, start and analyze benchmarks for molecular dynamics simulations.☆84Sep 5, 2024Updated last year
- A mini-course offered to Undergrad chemistry students☆21Dec 30, 2021Updated 4 years ago
- 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.
- The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation avai…☆407Updated this week
- the simple alchemistry test set☆10Nov 20, 2025Updated 8 months ago
- An open library for the analysis of molecular dynamics trajectories☆727Updated this week
- OpenMM plugin to define forces with neural networks☆220Jun 24, 2026Updated last month
- OpenMM plugin to interface with PLUMED☆82Jan 15, 2026Updated 6 months ago
- Set of tools to generate a multi-eGO force field to perform molecular dynamics simulations☆16Updated this week
- Compare optimized geometries and energies from various force fields with respect to a QM reference.☆14Apr 19, 2021Updated 5 years ago
- An open tool implementing some recommended practices for analyzing alchemical free energy calculations☆140May 24, 2024Updated 2 years ago
- A set of tutorials to introduce new users to the MoSDeF (Molecular Simulation Design Framework) toolkit☆27Apr 1, 2024Updated 2 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- A repository of update in molecular dynamics field by recent progress in machine learning and deep learning.☆344Jan 25, 2026Updated 6 months ago
- WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis☆217Updated this week
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆378Aug 5, 2026Updated last week
- Differentiable Markov Chain Monte Carlo☆15Mar 23, 2024Updated 2 years ago
- SIMD instructions for faster distance calculations.☆25Apr 7, 2026Updated 4 months ago
- The OpenMM Cookbook and Tutorials☆59Apr 28, 2026Updated 3 months ago
- TUPÃ: Electric field analyses for molecular simulations☆25Jun 12, 2026Updated 2 months ago
- MoleculeKit: Your favorite molecule manipulation kit☆238Updated this week
- MDToolbox.jl: A Julia package for molecular dynamics trajectories analysis and modeling of biomolecules☆23Mar 21, 2025Updated last year
- 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.
- Python implementation of the multistate Bennett acceptance ratio (MBAR)☆313Feb 12, 2026Updated 6 months ago
- A project (and object) for storing, manipulating, and converting molecular mechanics data.☆95Updated this week
- PDBFixer fixes problems in PDB files☆668Mar 10, 2026Updated 5 months ago
- Tools to build coarse grained models and perform simulations with OpenMM☆24Updated this week
- Collective variables library for molecular simulation and analysis programs☆242Updated this week
- Package to perform minimum-distance distribution analyses of complex solute-solvent interactions☆25Jul 28, 2026Updated 2 weeks ago
- MDAnalysis wrapper around Packmol☆37May 1, 2023Updated 3 years ago