MMAEVe: a Versatile Program for Constructing Systems for Molecular Dynamics Simulations and Visualization

28 August 2024, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Molecular dynamics simulations are commonly used for the study of membrane-protein systems. Current tools for building membrane-proteins systems are limited in their ability to incorporate multiple protein components in a set-up and their ability to operate using a variety of different forcefields for the lipid component. Here, we present a simple but effective membrane builder, MMAEVe, that can be used to construct massive protein-membrane systems of mixed composition. MMAEVe is open-sourced and available at https://github.com/AppleIntusion/MMAEVe, it is maintained and tested for Linux systems. A comprehensive tutorial and a benchmarking script are included with the source-code.

Keywords

Molecular Dynamics
Computational Chemistry
Membrane Simulation

Supplementary materials

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Supplemental Data
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A graphical depiction of point distributions and a benchmark table with more systems.
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Supplementary weblinks

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