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Updated: Jan 24, 2026

Automated Lipid Bilayer Membrane Formation Using a Polydimethylsiloxane Thin Film
Published on: July 10, 2016
PACKMOL-Memgen: A Simple-To-Use, Generalized Workflow for Membrane-Protein-Lipid-Bilayer System Building
Stephan Schott-Verdugo1,2, Holger Gohlke1,3
1Institute for Pharmaceutical and Medicinal Chemistry , Heinrich Heine University Düsseldorf , 40225 Düsseldorf , Germany.
Abstract:
We present PACKMOL-Memgen, a simple-to-use, generalized workflow for automated building of membrane-protein-lipid-bilayer systems based on open-source tools including Packmol, memembed, pdbremix, and AmberTools. Compared with web-interface-based related tools, PACKMOL-Memgen allows setup of multiple configurations of a system in a user-friendly and efficient manner within minutes. The generated systems are well-packed and thus well-suited as starting configurations in MD simulations under periodic boundary conditions, requiring only moderate equilibration times. PACKMOL-Memgen is distributed with AmberTools and runs on most computing platforms, and its output can also be used for CHARMM or adapted to other molecular-simulation packages.
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