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MEMBPLUGIN

Studying membrane complexity in VMD

MEMBPLUGIN is a membrane analysis tool for molecular-dynamics simulations. It is a collection of visual and command-line tools that can be run within the Visual Molecular Dynamics (VMD) environment to analyze biomolecular simulations of lipid bilayers.

Installation

Please see the Installation page and/or the INSTALL.txt file.

General usage

After installation, the plugin's Main Window is accessible from VMD's Extensions>Analysis>Membrane Analysis Tool (MEMBPLUGIN).

Note that all analysis is performed on-disk, not on the currently loaded molecule. If you modify your current molecule, e.g. to align it, make sure you save it on disk.

The systems to be analyzed have to satisfy certain constraints, notably they have to be oriented so that the bilayer normal is along the Z axis, and molecules need not be broken at the periodic cell boundaries. See details in the requirements list page.

Where atom selections are required, VMD's atom selection syntax applies. Additionally, the membplugin_lipids macro is available to indicate the residue names listed in the configuration, notably those supported by the CHARMM-GUI membrane builder.

Tools included

The following tools are currently included in MEMBPLUGIN. See the linked wiki pages for more information.

• The SCD Order Parameter Tool computes the Scd (deuterium order parameters) of lipid tails.
• The Membrane Thickness Tool computes bilayer overall thickness and its 2-D thickness map.
• The Interdigitation Tool measures the amount of interdigitation present between the two leaflets.
• The Area per Lipid Tool tool computes the average area per lipid of the membrane simulation along with the specific area per lipid of each lipid species.
• The Lipid Tilt Tool computes tilt angles with respect to the bilayer's normal.

Additionally, links are provided for the external Diffusion Coefficient and Density Profile tools.

Tutorial and case study

Two extended write-ups show the use of MEMBPLUGIN on realistic systems:

1. a step-by-step tutorial, suitable for beginners or first-time users; and
2. an advanced case study, showing the analysis performed on cholesterol-enriched membranes.

The documents are distributed together with the simulation data necessary to fully reproduce the analysis.

Command-line interface

All of the tools' functions can be accessed from VMD's scripting environment. The easiest way to learn about the syntax is to keep an eye on the console, where the equivalent TCL command is printed upon any calculation.

If you are in text-only mode, you might need to load mempluguin package first with 'package require membplugin'.

Run the following commands for usage info:

membranescd
lipidarea
interdigitation
lipidtilt
membranethickness

Citation

The plugin is described in the Bioinformatics paper MEMBPLUGIN: studying membrane complexity in VMD, which you should cite if you use this software in publications.

R. Guixà-González; I. Rodríguez-Espigares; J. M. Ramírez-Anguita; P. Carrió-Gaspar; H. Martinez-Seara; T. Giorgino; J. Selent. MEMBPLUGIN: studying membrane complexity in VMD. Bioinformatics 2014; vol. 30 (10) p. 1478-1480 doi:10.1093/bioinformatics/btu037

License

To use MEMBPLUGIN you need to comply with the terms of the GNU General Public License 3.0 (see the accompanying COPYING file).