[gmx-users] Restraints Riddle/Pull Puzzle

Christopher Neale chris.neale at alum.utoronto.ca
Mon Apr 4 18:18:48 CEST 2016

Possibilities that come to mind:

(1) absolute position restraints
(2) pull code distance restraints of each arm separately to the bottom of the U
(3) put 2x U-shaped proteins in the same box. It takes longer to simulate, but you get twice the sampling
(4) go back to the drawing board (this is likely what I would do).

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Trayder Thomas <trayder.thomas at monash.edu>
Sent: 04 April 2016 06:37
To: Discussion list for GROMACS users
Subject: [gmx-users] Restraints Riddle/Pull Puzzle

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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