[gmx-users] Restraints Riddle/Pull Puzzle

Trayder Thomas trayder.thomas at monash.edu
Mon Apr 4 12:37:53 CEST 2016

Okay, so...

I have a U shaped protein and the diameter of the U is larger than half the
shortest box vector. And it is already a huge box.
I want to prevent the U from straightening out.

My attempts at distance restraints fail because the shortest distance
between the ends of the U is across the periodic boundary (e.g. UU).

My attempts at pull code fail because, although the ends of the U are
closer to the COM of the U than the COM of the periodic image, there is no
suitable atom in the U for "pull-group1-pbcatom" and thus the COM is
calculated between periodic images.

Is there any trick to getting this to work using restraints/pull code?

Or is there another smart way to do this without increasing the box size?

Thanks in advance,

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