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

Marc Baaden baaden at smplinux.de
Sat May 10 17:04:01 CEST 2003

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   

create a situation where the lipids are extended to each side like:

 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 ?

Thanks in advance,

 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.marc-baaden.de
 FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217

More information about the gromacs.org_gmx-users mailing list