VMD-L Mailing List

From: Olaf Lenz (lenzo_at_mpip-mainz.mpg.de)
Date: Tue Dec 15 2009 - 03:38:55 CST

Hi!

On Monday 14 December 2009 08:37:36 pm Goutham wrote:
> I thouth pbc join would be a solution. But pbc join doesn't recognize
> options like -sel even in vmd 187.. Any pointers would be much appreciated.

Again, it is hard to understand your problem without snapshots or molecule
files. I try to guess what you want to be doing.

"pbc join" understands "-sel" since the very first version. However, it can
only be used to join molecules that have been broken, but it does not wrap
into different cells. To do that, you would have to use "pbc wrap" afterwards.
I would guess that you will need to do the following:

  # first join the chains
  pbc join chain

  # now wrap them into different unitcells
  pbc wrap -compound chain -sel "chain A"
  pbc wrap -compound chain -sel "chain B" -shiftcenterrel {1 0 0 }

Best regards
        Olaf 

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