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

[Anton Feenstra]

David wrote:
[...]
> genconf can be used in individual frames.
> 
> then you still have to cut out afterwards, but that is probably easiest.

Not if you want to keep whole molecules.
I've run into this when wanting/needing to extend or contract water
boxes, keeping the water around the protein and creating as little
disturbance in the whole system as possible. It'd be nice to have a
tool that could do this automatically, perhaps it could be an option
in genbox or genconf.

Meanwhile, what should work is the following:
1) use genbox -box to 'multiply' your original system. genbox has
    the advantage over genconf in that it will truncate your new system
    on the desired box size, and keep whole molecules.
2) if desired, re-center your protein with editconf, don't worry
    about lipids shifting out of the box, mdrun will take care of that,
    otherwise you can use trjconv to do that.


-- 
Groetjes,

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