[gmx-users] lipid bilayer: really no way to build it using GENCONF ??
mollica.luca at hsr.it
Thu Jul 10 11:52:01 CEST 2003
> 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
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