Membrane Generator (MemGen)
About:
MemGen is online web-service which generates multi-component lipid membranes for molecular dynamics simulations. MemGen is not restricted to certain force fields, lipid types, or MD simulation software. MemGen provides a PDB file of the membrane for download, which can be processed by any MD software. After uploading structure files of single lipid molecules, MemGen aligns these lipids along the Z-axis and creates a more compact structure of each one. This step in required to avoid atomic overlaps between adjacent lipids while setting up the membrane. Subsequently, MemGen generates the patch according to the requested number of lipids, mole fraction of lipid types, water molecules per lipid, and salt concentration. Counter ions are always added to neutralize the system.
Feature
MemGen should work with any all-atom or united-atom lipid, regardless of the type of head group or tails, or even the number of tails. MemGen developers tested MemGen with lipids containing between 1 and 6 tails, numerous different lipid types, common and unusual sterols, alcohol and detergent molecules. Only coarse-grained lipids are not supported. Note that the membrane structure provided by MemGen is highly ordered, so it requires energy minimization and careful equilibration. For membranes containing only one type of lipid plus water, 10 nanoseconds of equlibration are often enough. For multi-component membranes or systems containing ions, much longer equilibration may be required. Please check the equilibration from, for instance, the convergence of box dimensions and potential energy.
Download
MemGen is released as a free online service. The current version for all operating systems can be accessed form this link.
Citation
The preferred way to cite MemGen is:
- Christopher J. Knight and Jochen S. Hub MemGen: A general web server for the setup of lipid membrane simulation systems Bioinformatics, 31:2897-2899 (2015), doi:10.1093/bioinformatics/btv292.