CodeEntropy

CodeEntropy tool with POSEIDON code integrated to form a complete and generally applicable set of tools for calculating entropy

To run

Requirements

• Python > 3.6
• gcc
• g++

Install via

pip install .

Examples

See Example folder You can add your own trajectories by editing the path in the python script to point to your own trajectories

create_new_universe.py

This repo uses MDAnalysis to parse values and it can only parse force natively for GROMACS TRR and AMBER NETCDF. This scripts shows you how to create a new universe from unsuppported data so that you can use trajectories created from other simulation software or reduce the size of universe to focus on a section of simulation.

CodeEntropy_non_topo.py

Calculate entropy of target trajectory non topographical level

CodeEntropy_topo.py

Calculate entropy of target trajectory based on different method

Poseidon_GROMACS

!!! the trajectories are not included in this repo due to file size limit. Run POSEIDON analysis for a GROMACS trajectories

Poseidon_LAMMPS

A LAMMPS example for POSEIDON

mcc_mdanalysis

A DNA example for CodeEntropy

mcc_mdanalysis_multiprocess

mcc_mdanalysis with multiprocess parallelization

Copyright

Copyright (c) 2022, DonaldChung-HK

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.6. Modified from arghya90/CodeEntropy version 0.3