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