Matthieu Chavent, Tyler Reddy, Joseph Goose, Anna Caroline E. Dahl, John E.
Stone, Bruno Jobard, and Mark S.P. Sansom.
Methodologies for the analysis of instantaneous lipid diffusion in
MD simulations of large membrane systems.
Faraday Discussions, 169:455-475, 2014.
(PMC: PMC4208077)
CHAV2014-JS
Interactions between lipids and membrane proteins play a key role in determining the
nanoscale dynamic and structural properties of biological membranes. Molecular dynamics
(MD) simulations provide a valuable tool for studying membrane models, complementing
experimental approaches. It is now possible to simulate large membrane systems, such as
simplified models of bacterial and viral envelope membranes. Consequently, there is a
pressing need to develop tools to visualize and quantify the dynamics of these immense
systems, which typically are comprised of millions of particles. To tackle this issue, we
have developed visual and quantitative analyses of molecular positions and their velocity
field using path line, vector field and streamline techniques. This allows us to highlight
large, transient flowlike movements of lipids and to better understand crowding within the
lipid bilayer. The current study focuses on visualization and analysis of lipid dynamics.
However, the methods are flexible and can be readily applied to e.g. proteins and
nanoparticles within large complex membranes. The protocols developed here are readily
accessible both as a plugin for the molecular visualization program VMD and as a module
for the MDAnalysis library.
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