[gmx-users] output unimaged trajectory?

david.evans at ulsop.ac.uk david.evans at ulsop.ac.uk
Wed Jul 14 11:00:22 CEST 2004

Thanks for replying, probably these questions are insignficant, but I
would like to understand anyway.

>I don't know what unimaged means exactly.

I mean with the coordinates of all atoms propagated continuously in
3D space, not wrapped around to the other side of the periodic box
when they cross a boundary. 

>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
>otherwise it will translate (unless your systems consists of only one

This is where Amber and Gromacs seem to give different results. I'm
removing (according to my understanding of the docs  of both
programs) the motion of the centre of mass of the whole system
(water+solute). Amber, which outputs 'unimaged' trajectories, gives
an untranslating solute molecule, with the waters moving gradually
away from it in all directions. In gromacs the solute translates.

>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).
This being the case, it suggests to me that there is some difference
I don't understand between how the COM motion is removed in the two
programs. Probably this makes no difference to any actual result, but
I 'd like to understand everything before I start my huge batch of
simulations :)

>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.

Actually that is the precise issue of my original question! Amber by
default doesn't put them back on the other side (what I'm calling
unimaged trajectories), whereas Gromacs does. Amber has an option to
change to the other behaviour, but does Gromacs ?.... This might help
me see what is going on.



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