posted on 2021-08-27, 21:03authored byPaul Smith, Christian D. Lorenz
Molecular
dynamics simulations are now widely used to study emergent
phenomena in lipid membranes with complex compositions. Here, we present
LiPyphilica fast, fully tested, and easy-to-install Python
package for analyzing such simulations. Analysis tools in LiPyphilic
include the identification of cholesterol flip-flop events, the classification
of local lipid environments, and the degree of interleaflet registration.
LiPyphilic is both force field- and resolution-agnostic, and by using
the powerful atom selection language of MDAnalysis, it can handle
membranes with highly complex compositions. LiPyphilic also offers
two on-the-fly trajectory transformations to (i) fix membranes split
across periodic boundaries and (ii) perform nojump coordinate unwrapping.
Our implementation of nojump unwrapping accounts for fluctuations
in the box volume under the NPT ensemblean
issue that most current implementations have overlooked. The full
documentation of LiPyphilic, including installation instructions and
links to interactive online tutorials, is available at https://lipyphilic.readthedocs.io/en/latest.