From: Anton Arkhipov (
Date: Sun Dec 06 2009 - 00:35:46 CST

Hi Francesco,

Just to add to whatever help you got already:

for an rbcg bilayer, take an equilibrated all-atom bilayer, and
convert it to rbcg. If you want to be extra careful, then you can
solvate the result with rbcg water and use rbcg simulation to
equilibrate the bilayer further.

For sbcg, there's no direct conversion available, but it's not
necessary, because the model is extremely simple - just two beads
connected by a spring make one "molecule", and a bunch of such
molecules constitute a leaflet. So if you need an sbcg bilayer, it's
very simple to just create a pdb with such molecules by hand. You cna
put those sbcg "molecules" uniformly distributed in the bilayer, and
then equilibrate them with sbcg simulations.


On Dec 2, 2009, at 10:13 AM, Francesco Pietra wrote:

> Hi;
> After I posted the subject problem as secondary matter, I carried out
> an accurate search on the web, unable to find an equilibrated rbcg
> lipid bilayer for vmd 1.8.7/namd martini implementation (or a plain
> procedure to get it from scratch). As for sbcg, I guess that direct
> conversion from an equilibrated all-atoms lipid bilayer will not work.
> Thanks for info.
> francesco pietra