Analysis without phases

While ML-LPA has been ultimately designed and developed to analyse the lipid phases, the tools used to analyse the local environment can be used investigate other types of environment than the phases.

Setting

In this tutorial, we will see how to do that by analysing a mixture of DLPC and DOPC, with some cholesterol inserted in the bilayer. At room temperature, both molecules are found in the fluid phase, so doing a ML prediction here is supposedly meaningless. Instead, we want to check if the cholesterol has a preference for the double bonds of the DOPC molecules or not.

Performing the analysis

The codelines of the whole analysis are given below. Comments have been added to help understanding the process.

1
2
3
4
5
6
7
8
9
10
11
12
13
14
import mllpa

# Load the simulation files and extract the three systems of interest
unknown_system_dlpc = mllpa.openSystem('unknown.gro', 'unknown.tpr', 'DLPC')
unknown_system_dopc = mllpa.openSystem('unknown.gro', 'unknown.tpr', 'DOPC')
unknown_system_chol = mllpa.openSystem('unknown.gro', 'unknown.tpr', 'CHL1')

# Assign manually the label of the molecules
unknown_system_dlpc.setPhases("saturated")
unknown_system_dopc.setPhases("unsaturated")
unknown_system_chol.setPhases("cholesterol")

# Do the tessellation of the bilayer in 3D - we exclude the cholesterol from the ghost generation
unknown_tessellation = mllpa.doVoro([unknown_system_dlpc, unknown_system_dopc, unknown_system_chol], geometry='bilayer_3d', exclude_ghost=[2])

All the results have been saved in the instance of the Tessellation class named unknown_tessellation here. More details can be found in a previous tutorial.

What is next?

Now that the local environment has been mapped, the last step is to save all the results in a file.

Check the API

The following elements have been used in this tutorial: