About MemGen

MemGen generates multi-component lipid membranes for molecular dynamics simulations.

If you use structures generated by MemGen for a publicaiton, we kindly request that you cite this article:

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  

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.


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. We 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.

Privacy

MemGen does not require you to submit an email address or any other personal information.

We keep the results of your job in the system for 28 days in case you need to re-download or share the link, after which time it will expire.

The people behind MemGen

Christopher J. Knight developed the website's front end, design, initial input processing, and lipid delineation. Jochen S. Hub designed the concept of MemGen and wrote the scripts involved in molecular modelling. The website is hosted by the GWDG. This project was supported by the Deutsche Forschungsgemeinschaft (Emmy-Noehter Program and SFB 803/A12).