https://github.com/bio-phys/cnt-lipid14-analysis

Analysis tools for simulations of carbon nanotubes (CNTs) in lipid membranes modeled with the Lipid14 force field.
https://github.com/bio-phys/cnt-lipid14-analysis

Last synced: 5 months ago
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Analysis tools for simulations of carbon nanotubes (CNTs) in lipid membranes modeled with the Lipid14 force field.

• Host: GitHub
• URL: https://github.com/bio-phys/cnt-lipid14-analysis
• Owner: bio-phys
• License: gpl-3.0
• Created: 2018-02-02T13:50:47.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2019-12-10T02:32:37.000Z (over 6 years ago)
• Last Synced: 2025-09-09T19:34:52.662Z (9 months ago)
• Language: Python
• Size: 25.4 KB
• Stars: 3
• Watchers: 3
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

          
# This project contains

Analysis of Lipid14 simulations

 - order14.py: Calculates the deuterium order parameter of the lipids (works without CNT).

Analysis of Lipid14 simulations with a CNT

 - order14distance.py: Calculates the order parameter as a function of the annular shell around the CNT axis.

 - order14distance-manyCNTs: same as above, but adds a category for lipids shared between two CNTs.

 - cntmotion.py: Calculates the COM motion and the tilting angle of a CNT (works with any lipids).

 - rdf14.py: Calculates the radial distribution of a given atom type aroud the CNT axis.

Required geometry functions

 - geometry.py

#  Requirements: 

 - Python 2.7

 - Python packages: sys, argparse, numpy, scipy, MDAnalysis

# Literature

 - M. Vögele, J. Köfinger, G. Hummer: 

   Simulations of Carbon Nanotube Porins in Lipid Bilayers.

   Faraday Discuss., 2018, Accepted Manuscript, DOI: 10.1039/C8FD00011E  

   http://pubs.rsc.org/en/content/articlelanding/2018/fd/c8fd00011e