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

Marc Baaden baaden at smplinux.de
Mon May 12 15:21:00 CEST 2003

>>> Anton Feenstra said:
 >> OK, then, why not use trjorder to sort your lipids on distance to the
 >> protein? [..]
 >> Or whould this not give enough bilayer in all directions?

I think that is the problem. If you take the closest lipids, I fear that
in one direction (let's say y) it will be a bit too few, in particular as
you divide the thickness of the y-layer by 2, as you put part of the lipids
at +y with respect to the protein and part of them at -y.

So, in particular in that y-direction I would like to take into account a
lipid and its periodic copy to avoid any discontinuities for analysis.


 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