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chromatophore_large_system_simulation icon chromatophore_large_system_simulation

Contain herein are scripts for making an all atom model of a chromatophore from Rhodobacter sphaeroides, as well as configuration scripts for MD and BD simulations of the aforementioned model using the simulation package NAMD. Additionally, there are scripts to run APBS calculations.

develop-mcce icon develop-mcce

This repo is code under development, some parts may not work properly.

mcce_benchmarking icon mcce_benchmarking

For benchmarking MCCE experiments viz experimental pKas or viz other MCCE experiments (A/B testing)

mcce_crgms icon mcce_crgms

For developing charge analysis with correlation and top_N charge microsstates csv creation

mcce_protinfo icon mcce_protinfo

Provide information about a protein pdb file on its structure and issues flagged in the run.log produced by MCCE's step1.py.

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