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

[Björn Sommer]

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):
http://Cm2.CELLmicrocosmos.org

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:

http://www.cellmicrocosmos.org/Cmforum/viewtopic.php?f=21&t=641&p=1348&hilit=vmd#p1348

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

http://www.ncbi.nlm.nih.gov/pubmed/24688707

If you have questions, let me know.

Have fun!
Bjorn