Path D - Module 40: PBC Geometry & Conventions

Membrane simulations are highly sensitive to PBC. In this module, you will learn to manage the semi-isotropic box scaling of a lipid bilayer.

import molsysmt as msm
from molsysmt import systems
system = systems['POPC membrane']['popc_membrane.h5msm']
box = msm.get(system, element='system', box=True)
print(f"Membrane Box:\n{box}")

Box parameters and volume

MolSysMT reports box lengths in nanometers and computes the volume directly from the lengths and angles.

lengths, angles = msm.pbc.get_lengths_and_angles_from_box(box)
volume = msm.pbc.get_volume_from_lengths_and_angles(lengths, angles)
print(f"Box lengths: {lengths}")
print(f"Box angles: {angles}")
print(f"Box volume: {volume}")