[gmx-users] lipid bilayer: really no way to build it using GENCONF ??

[Luca Mollica]

> Well, it has been proven to work, but only quite recently.
> First, have you checked Peter Tieleman's website, to see if your
> favorite lipid is there?

Yes, I have, and found too(128POPC)....but, being a beginner, build mono 
and double layers could be a good exercise for understanding topology 
and topology files, problems related to layers, etc ..... :-)


> Second, yes use genconf! To make it relatively fast you could start out
> with something small, say 32 lipids (16+16) use genconf to make the two
> 4x4 lattices, put them together manually then just add a little bit of
> water (say 1 nm), and simulate with tight pressure coupling and only a
> short cut-off (e.g. 0.9 nm). Simulate until you have reasonable density
> (and separate phases). Then you can think of extending the lipid layer
> to 64+64, add more water and use PME.


Right, this was quite the same idea I had: but I only wanted to check if 
there was or was not an option to build a double layer skipping 
simulation. GENCONF command works really  "like a small child playing 
with wooden blocks", and what I obtain with a 8 X 8 X 2 grid a is a 
isoriented double layer, far from chemistry and reality!!!
Now, I know that a set of simulation has to be performed, let me try to 
do it!

Thank you

Luca