[gmx-users] dopg

Martina Bertsch, PhD mbe404 at lulu.it.northwestern.edu
Fri Feb 13 23:41:01 CET 2004

Greetings, Lakshmi.

First, build a single DOPC/DOPG molecule in InsightII or Sybyl. Then, 
use genconf to build a small starting bilayer.

The following is a protocol from a recent discussion between Luca 
Mollica and David van der Spoel that might interest you.


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. 


Lakshmi Padmavathi wrote:

>Dear gromacs users,
>  could anybody suggest me how to prepare a bilayer with dopc,dopg(70:30) and 
>water. where can i get the pdb files of dopg and dopc. 
>all suggestions are welcome.
>thank you very much.
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