CALVADOS_Analysis: Advanced Tools for Coarse-Grained Molecular Dynamics Analysis¶
I'm excited to share a new Python package I've been working on called CALVADOS_Analysis. This toolkit is designed for comprehensive analysis of coarse-grained molecular dynamics simulations, with a particular focus on CALVADOS models and similar systems.
What is CALVADOS_Analysis?¶
CALVADOS_Analysis is a specialized package that helps researchers extract meaningful insights from molecular dynamics simulations. It provides a suite of analytical tools to understand complex biomolecular systems through various computational lenses.
Key Features¶
- Cluster Analysis: Track formation, size distribution, and evolution of molecular clusters
- Contact Networks: Generate detailed contact maps and interactive network visualizations
- Structure Factor Analysis: Quantify structural organization with sophisticated structure factor calculations
- Diffusion Analysis: Measure molecular mobility and diffusion coefficients
- Density Analysis: Analyze phase separation with slab density profiles and Flory-Huggins theory fitting
Performance Optimization¶
The package leverages multiprocessing capabilities to significantly accelerate computations, making it practical for analyzing large simulation datasets. Most modules include parallel processing to efficiently handle thousands of trajectory frames.
Visualization¶
CALVADOS_Analysis generates publication-quality visualizations including:
- Contact network graphs
- Cluster size violin plots
- Time evolution charts
- Structure factor plots
- Phase separation density profiles
I'll be posting more detailed tutorials about specific features in upcoming blog posts. If you work with coarse-grained simulations, especially for phase separation systems, I'd love to hear your feedback on the package!