[gmx-users] Regarding Lipid bilayer genration (Bikash Ranjan Sahoo)

Björn Sommer bjoern at CELLmicrocosmos.org
Sat Feb 20 21:15:37 CET 2016

Hi Bikash,

yeah, you can try CharmmGui. If it fails to create this small system, 
you can use our MembraneEditor with the Packing Algorithm Distributer 
and define the number of lipids you want to have. You will have to check 
which membrane size you want. Just check the are per lipid.

Get here the tool (got to start - you need Java preinstalled):

You will also find some tutorials there. Make sure that you change the 
PDB Export Properties in the way that it is Gromacs compatible. And then 
apply the standard protocol. editconf, genbox, (genion?), grompp, mdrun

Because your system is quite small you might have problems with the 
water inside your membrane layers. Just throw it out with VMD after 
doing genbox, you find here the info, how to do this:


Do not forget to update the topology regarding the number of water atoms.

You can also use PackMol, but then you have to do some scripting. I once 
wrote a small open access article about that


If you have questions, let me know.

Have fun!

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