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