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

[David van der Spoel]

On Thu, 2003-07-10 at 10:11, Luca Mollica wrote:
> Dear all users,
> 
> I'm tryng to build a lipid double layer by myself(using GENCONF 
> command), and, looking for advices and some help inside this mailing 
> list, I've found a November 30th 2002 mail titled "Am I wrong ?", whose 
> text(the final part) is reported below:
> 
> ------
> 
> Genconf is fine, but very crude. You can also just mix the lipids and
> water and let it go, after some NS (10-50) you will probably have a nice
> bilayers.
> 
> ------
> 
> Really? Well, a 10-50 ns simulation is very machine time expensive, and 
> by now(I'm only a beginner in MD) I'm working on one machine only!
> Is there a more straightforward way to build a double layer(no problems 
> with GENCONF command in order to build a monolayer....)?

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?

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.

> 
> Thank you all in advance,
> 
> Luca
> 
> 
> 
> 
> 
> *******************************************************************************************************
> 
> Luca Mollica
> Dulbecco Telethon Institute (Protein Structure Laboratory)
> c/o Cellular and Molecular Neurobiology
> DIBIT-HSR,Via Olgettina 58
> 20132 Milano (Italy)
> 
> Tel: 0039-02-26434824
> Fax: 0039-02-26434813
> E-mail: mollica.luca at hsr.it
> 
> DTI website: http://www.telethon.it/dti/
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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