[gmx-users] pull_geometry=direction

Christopher Neale chris.neale at alum.utoronto.ca
Thu Jan 9 18:06:04 CET 2014

Try using
pull_geometry = direction-periodic

For more details, see http://bugzilla.gromacs.org/issues/1352

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Lalita Shaki <lalitashaky at gmail.com>
Sent: 09 January 2014 10:34
To: gmx-users
Subject: [gmx-users] pull_geometry=direction

Dear gromacs users,

I have been working on a pulling simulation of the unfolding of a protein
and I have found out that went using pull_geometry=direction the code
checks at each time step if the groups distance is  higher than 0.49 each
of the dimensions of the box. If the distance is higher that 0.49 of at
least one of the dimensions the simulations ends in an error. So pretty
much when you want to unfold a protein you would have to use a really large
cubic box.

My question is if someone knows why gromacs check the magnitude of the
distance again the dimension of the box and does not check each of the
components of the distance vector to it correspondent dimension of the box.
I think this will also avoid the problem of miss calculating the
 pull-reference distance and at the same time will permit to run
calculations with a rectangular box.

Thank you


Lalita S. Uribe.
European Master in Theoretical Chemistry and Computational Modeling.
PhD student. Johannes Gutenberg-Universität Mainz
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