Tools for coarse-grained molecular dynamics simulations using the SPICA force field
☆13May 12, 2026Updated 2 weeks ago
Alternatives and similar repositories for spica-tools
Users that are interested in spica-tools are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Example files for Colvars module: https://github.com/Colvars/colvars☆14Dec 7, 2021Updated 4 years ago
- Perform polymerization and crosslinking in MARTINI coarse-grained forcefield using GROMACS MD package☆29Jan 21, 2026Updated 4 months ago
- ☆11May 12, 2026Updated 2 weeks ago
- Coarse grain to atomistic molecular coordinate and topology converter☆16Mar 13, 2025Updated last year
- Massively parallel hybrid particle-field molecular dynamics in Python.☆30Sep 6, 2024Updated last year
- 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.
- ☆10Oct 28, 2022Updated 3 years ago
- Optimization tool for calibrating coarse-grained force fields of lipids, relying on the simultaneous usage of reference AA trajectories (…☆10Jun 6, 2023Updated 2 years ago
- Gibbs sampling for expanded ensembles and replica exchange simulations☆11Jun 1, 2014Updated 11 years ago
- Software for automated processing of alchemical free energy calculations☆12Nov 7, 2022Updated 3 years ago
- Force field-inspired molecular representation learning model☆22Sep 26, 2023Updated 2 years ago
- Repository for PFRED GUI codes☆10Feb 25, 2020Updated 6 years ago
- Molecular visualization for MDAnalysis with MolecularNodes in Blender☆21Mar 30, 2025Updated last year
- Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates☆189May 8, 2026Updated 2 weeks ago
- The Vini in silico model of cancer☆12Mar 7, 2026Updated 2 months ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Cyclic-peptide - protein complexes benchmark and associated scripts and data☆15Aug 31, 2024Updated last year
- Collection of interaction and molecule parameters for the Martini3 force-field☆21Feb 7, 2023Updated 3 years ago
- ☆21Aug 16, 2019Updated 6 years ago
- HAL's MD package: Highly Accelerated Large-scale Molecular Dynamics simulations☆24Oct 2, 2025Updated 7 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
- ☆15Sep 5, 2025Updated 8 months ago
- Fast, parallelized implementation of Principal Component Analysis with constant memory consumption for large data sets.☆12Feb 18, 2022Updated 4 years ago
- ☆16Dec 24, 2016Updated 9 years ago
- mirror of https://zhanglab.ccmb.med.umich.edu/EDTSurf/☆10Jun 20, 2023Updated 2 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling metho…☆24Sep 26, 2024Updated last year
- Generative backmapping of coarse-grained molecular systems using an equivariant graph neural network and flow-matching☆12Sep 17, 2025Updated 8 months ago
- Python code to run Thermal Titration Molecular Dynamics (TTMD) simulations☆20Feb 25, 2026Updated 3 months ago
- KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.☆35Jan 6, 2026Updated 4 months ago
- A collection of tools for DNA modelling☆25Apr 9, 2026Updated last month
- Calculates 3d structure factor and simulated x-ray diffraction pattern from molecular dynamics trajectories☆18Nov 21, 2019Updated 6 years ago
- SIEVE-Score: interaction energy-based virtual screening method based on random forest.☆14Sep 15, 2023Updated 2 years ago
- A Python library for constructing polymer topologies and coordinates☆22Sep 23, 2025Updated 8 months ago
- Gromacs to Lammps simulation converter☆93Dec 9, 2023Updated 2 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Describe and apply transformation on molecular structures and topologies☆144May 5, 2026Updated 3 weeks ago
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆16Jan 20, 2022Updated 4 years ago
- ☆52Jul 16, 2025Updated 10 months ago
- ☆65Dec 10, 2025Updated 5 months ago
- Pymolsnips is a library of PyMOL scripting language code fragments for several popular text editors.☆43May 8, 2024Updated 2 years ago
- Quantifying the nativeness of antibody sequences using long short-term memory networks☆18Dec 17, 2021Updated 4 years ago
- Automatic generation of LAMMPS data file for atomistic and coarse-grained simulations of molecular and polymeric materials with various t…☆20Mar 24, 2026Updated 2 months ago