[gmx-users] output unimaged trajectory?
gmx3 at hotmail.com
Wed Jul 14 10:36:48 CEST 2004
>From: david.evans at ulsop.ac.uk
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] output unimaged trajectory?
>Date: Wed, 14 Jul 2004 09:18:42 +0100
>Thanks for the reply. I have been using `trjconv -pbc nojump', but
>the molecule then appears to translate through the system, in
>contrast to the same system simulated in Amber. I want to know if
>this is because of the imaging or whether there is a real physical
>difference between the two MD engines. I've tried to make the input
>parameters as compatible as possible, particularly the centre of mass
>So, the main question was about mdrun, which seems to output imaged
>trajectories by default. Could you confirm that it is impossible to
>get mdrun to output unimaged coordinates?
I don't know what unimaged means exactly.
But what you are refering to here are two different things.
Whether or not molecules translates through the box depends only
on the choice of center of mass motion removal groups.
If a molecule is a single center of mass motion removal group and
center of mass motion is removed it will not translate through the box,
otherwise it will translate (unless your systems consists of only one
Any type of imaging (in mdrun or trjconv) will not make a molecule
which is a center of mass motion removal group move
(unless you let trjconv center on a moving group).
The only choice according to me (unless Amber does something strange)
is what you do with molecules that move out of the primary cell,
do you put them back on the other side (which causes jumps) or not.
But as I understood that is not the issue here.
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