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

[Anton Feenstra]

Marc Baaden wrote:
> Hi,
[...]
> 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.

OK, then, why not use trjorder to sort your lipids on distance to the
protein? That would be independent on any rotation/translation/fitting,
and you can always re-apply the pbc and put all molecules back into the
box, as long as you use the box from the actual trajectory frame.

Or whould this not give enough bilayer in all directions?


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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