[gmx-users] Creating a layer bigger than one PBC

[David]

On Sat, 2003-05-10 at 17:03, Marc Baaden wrote:
> Sorry for the somewhat incomprehensible title. It is the clearest
> I could come up with.
> 
> Following problem: I have a protein in a lipid
> bilayer and create a protein+lipid trajectory for analysis. I use
> re-centering on the protein and then create an adjusted periodic box
> with whole molecules (-pbc whole).
> 
> But the lipids jump obviously from time to time, which makes the
> lipid belt quite variable in size (note that periodicity is lost
> due to fitting including rotation to a protein conformation, so one
> can no longer use periodic conditions at that point).
> 
> So what I would like is instead of having the following:
> 
> 
> +----------+
> |LLLLLLLLLL| <- periodic box,  L=lipid   P=protein   
> |LLLLPPPLLL|
> |LLLLLLLLLL|
> +----------+
> 
> create a situation where the lipids are extended to each side like:
> 
>  LLLLLLLLLL   <-+
>  LLLLLLLLLL     |  <-+
>  LLLLPPPLLL     |    |
>  LLLLLLLLLL   <-+    | duplicate "copies"
>  LLLLLLLLLL        <-+
> 
> So that I can cut out a homogeneous belt around the protein.
> 
> Any hint how to get there with existing Gromacs tools ?
genconf can be used in individual frames.

then you still have to cut out afterwards, but that is probably easiest.

> 
> Thanks in advance,
>   Marc
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular 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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