It is assumed the reader has already compiled espressomd and is familiar with its basic usage. If not, see installation and a brief tutorial.
Detailed information about the Cooke lipid model can be found in the following papers:
- Original 3-bead model: Cooke & Deserno JCP 2005
- Flip-fixed 4-bead model: Foley & Deserno JCTC 2020
Lipid.py and mbtools.py comprise the "pymbtools" suite of tools. Lipid.py contains the definiton for the Lipid class and mbtools.py is a collection of functions for assembling lipid bilayers in various geometries, along with a few rudimentary analysis functions and a method for bonding together particles into large-scale rigid structures.
The template directory contains 5 example scripts that run short simulations demonstrating the functionality of pymbtools.
-
flat_3bead.py: The simplest case. A flat, 3-bead (original) Cooke model membrane. -
flat_flipfixed.py: Still just a flat periodic membrane, but with the updated (4-bead) Cooke model which suppresses flip-flop. This can be use to simulate asymmetric membranes. -
buckle.py: 4-bead flipfixed Cooke membrane buckled along the x-direction of the simulation box. -
stickytape.py: This shows how to run a simulation of a membrane strip with open edges patched up with "stickytape" (see Foley & Deserno JCP 2024). Additionally, this file includes code for making 4-bead Cooke lipids with varying aspect ratios using an angle for tapering in order to open up the field of curvature-asymmetric membranes. This version constructs the stickytapes the hard way, manually placing each individual bond in a thought-out way to form a rigid cross-linked structure. -
stickytape_autobond.py: This simulation is very similar to the previous one, but makes use of mbtools' springBondStructure() to automatically bond together all stickytape beads within a particular cutoff distance of one another, making the task of creating a rigid structure much easier.