[gmx-users] pull_geometry=direction

Lalita Shaki lalitashaky at gmail.com
Fri Jan 10 09:51:32 CET 2014

Dear Christopher and gromacs users,

I consider using the pull_geometry = direction-periodic. nut this option
prevent me to use any pressure scaling, which I am not sure it is good for
my calculation.

Does someone can recommend me some literture about the effect of using the
NVT ensemble or the NPT one?

Is there any major difference between pull_geometry = direction-periodic
and pull_geometry = direction?

Thank you


Message: 1
Date: Thu, 9 Jan 2014 16:32:27 +0000
From: Christopher Neale <chris.neale at alum.utoronto.ca>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] pull_geometry=direction
73733370c76c466583ceaa4f2041076a at BLUPR03MB184.namprd03.prod.outlook.com>

Content-Type: text/plain; charset="iso-8859-1"

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-Universit?t Mainz

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

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