[gmx-users] Regarding Lipid bilayer genration (Bikash Ranjan Sahoo)
bjoern at CELLmicrocosmos.org
Sat Feb 20 21:15:37 CET 2016
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.
More information about the gromacs.org_gmx-users