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

Marc Baaden baaden at smplinux.de
Mon May 12 14:38:01 CEST 2003


although I can see where you are getting, let me just re-scpecify
my original question. It was actually not aimed at creating a new
system, but in analyzing an existing trajectory ..

What I want for my analysis is the protein in the center, with as
much lipid around it as is in the simulation system. Eg from my central
protein to the next periodic copy of it let's say, in all 3 directions.
And then cut out again a given layer.

I think it is quite tricky, because some lipids will be present as
2 periodic copies, which bears problems I guess for topology/tpr to
structure assignments.

Let me re-phrase again: let's say you take your fully periodic system,
eg central box plus surrounding ones, and you choose one protein in the
middle. Then take from this central protein, an additional continuous
lipid belt of maximum thickness. I'd like to be able to create such a
trajectory and use it for analysis.

>>> Anton Feenstra said:
 >> David wrote:
 >> [...]
 >> > genconf can be used in individual frames.
 >> > then you still have to cut out afterwards, but that is probably easiest.
 >> [..] It'd be nice to have a
 >> tool that could do this automatically, perhaps it could be an option
 >> in genbox or genconf.
 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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