automate the setup of atomistic clay models for classical molecular dynamics simulations with GROMACS
☆20Oct 14, 2025Updated 9 months ago
Alternatives and similar repositories for ClayCode
Users that are interested in ClayCode are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A GROMACS implementation of the ClayFF force field☆43Dec 28, 2022Updated 3 years ago
- A force field for the simulation of inorganic-organic interfaces (INTERFACE-CHARMM, INTERFACE-PCFF)☆23Feb 14, 2024Updated 2 years ago
- Atomistic Topology Operations in Matlab, scripts for manipulation of molecular dynamics or monte carlo simulation systems☆23Nov 27, 2025Updated 8 months ago
- Python program for modelling and simulating polymers.☆44Jul 6, 2026Updated last month
- A set of tutorials to introduce new users to mBuild☆11Jun 14, 2021Updated 5 years ago
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- A dissipative particle dynamics (DPD) project.☆13Aug 16, 2023Updated 2 years ago
- Stable AutoCorrelation Integral Estimator☆17May 18, 2026Updated 2 months ago
- pyCSH: automated generation of realistic bulk calcium silicate hydrate (C-S-H) structures.☆13Jun 26, 2024Updated 2 years ago
- Repository with conda recipes for LAMMPS, GROMACS, etc (WIP)☆11Apr 11, 2024Updated 2 years ago
- Source code for "Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome inter…☆13Jun 17, 2022Updated 4 years ago
- ☆50Jun 15, 2020Updated 6 years ago
- Python-based tool to calculate instantaneous interfaces and concentration/orientation profiles from molecular simulation trajectories in …☆12Nov 5, 2019Updated 6 years ago
- Neural functional theory for inhomogeneous fluids - Tutorial☆16May 20, 2025Updated last year
- Optimize classical force field parameters against reference data☆12Jul 23, 2026Updated 2 weeks 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.
- Automatic generation of LAMMPS data file for atomistic and coarse-grained simulations of molecular and polymeric materials with various t…☆25Aug 3, 2026Updated last week
- Coarse grain to atomistic molecular coordinate and topology converter☆16Mar 13, 2025Updated last year
- Stochastic first-passage time (FPT) simulations using importance sampling.☆10Oct 2, 2024Updated last year
- Code to compute Onsager transport coefficients from molecular dynamics simulations using mean-square displacements.☆29Jun 15, 2021Updated 5 years ago
- Graph-Based Force Fields Model to parameterize Force Fields by Graph Attention Networks☆10Apr 9, 2024Updated 2 years ago
- Tools for polymer molecular dynamics simulations☆16Jul 20, 2026Updated 3 weeks ago
- SMolSAT.py: Soft-Matter Molecular Simulation Analysis Toolkit☆15Dec 17, 2024Updated last year
- A Python/Fortran order parameter analysis library☆14Dec 22, 2020Updated 5 years ago
- Generate coarse-grained molecular dynamics models from atomistic trajectories.☆68Aug 2, 2026Updated last week
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Playmol is a(nother) software for building molecular models☆19Mar 14, 2023Updated 3 years ago
- A set of tutorials to introduce new users to the MoSDeF (Molecular Simulation Design Framework) toolkit☆27Apr 1, 2024Updated 2 years ago
- Code and examples to compute IR spectra from normal mode analysis☆15Jul 28, 2022Updated 4 years ago
- Analyse Rotational Diffusion Tensor from MD Simulations☆22Oct 31, 2024Updated last year
- ☆14Jun 4, 2024Updated 2 years ago
- A Set of Tutorials for the LAMMPS Simulation Package☆47Apr 10, 2026Updated 4 months ago
- ☆21Apr 26, 2026Updated 3 months ago
- A molecular dynamics tutorial for new researchers in the area of nanomechanics.☆16Sep 2, 2022Updated 3 years ago
- This package is meant to calculate the dihedral entropy of a biomolecule. However, it can also calculate the entropy of any binnable dat…☆24Feb 2, 2024Updated 2 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-…☆49Aug 19, 2024Updated last year
- Molecular Dynamics in the Open☆90Updated this week
- The computational modeling tool for custom atomistic model of calcium-silicate-hydrates (C-S-H)☆23May 14, 2023Updated 3 years ago
- Coarse-grained mapping and parametrisation for the Martini 3 forcefield☆23Jul 20, 2026Updated 3 weeks ago
- 2D and 3D wormlike chain generator for Python and written in C++☆19May 26, 2025Updated last year
- Machine learning exercises for the MolSim course (http://www.acmm.nl/molsim/molsim2023/index.html)☆29Jan 16, 2024Updated 2 years ago
- Main code repository for the PLUMED-GUI plugin for VMD☆17Jan 22, 2026Updated 6 months ago