[gmx-users] Difference between output_coordinates.gro and trajectory.xtc coordinates

[Mark Abraham]

Hi,

On Wed, Jun 21, 2017 at 6:49 PM Diez Fernandez, Amanda <
amanda.diez10 at imperial.ac.uk> wrote:

> Hi Justin,
> Thank you for your reply.
>
> Here are the links to the images of:
> -the output coordinates
> -and last frame of trajectory.
>
> Output coordinates which look wrong:
> http://i1036.photobucket.com/albums/a443/amanda222lld/output_coordinates_zp
> stuqkgjd2.png
> <http://i1036.photobucket.com/albums/a443/amanda222lld/output_coordinates_zpstuqkgjd2.png>
>
> Last frame from trajectory which looks OK:
> http://i1036.photobucket.com/albums/a443/amanda222lld/last_frame_traj_zpsn2
> 7nzusn.png
> <http://i1036.photobucket.com/albums/a443/amanda222lld/last_frame_traj_zpsn27nzusn.png>
>
> For the last frame of the trajectory I used trjconv -pbc nojump to make
> sure the atoms were not being wrapped around the box.


That's what you're getting. See "gmx help trjconv" where it specifically
says that "-pbc nojump" will lead to atoms appearing to diffuse out of the
box.

It seems like you want trjconv -pbc atom, so all the atoms are in the same
box. That won't necessarily match what mdrun -c writes, either, because
that is not something for which we have designed. There's an infinite
number of equivalent representations of any system, and a large number of
plausible representations that someone might want to use for different
purposes, so we've left the choice to you, with the tools and documentation
to get something that makes you happy :-)

Mark