[gmx-users] Trajectories not centered

[Mark Abraham]

Hi,

You've asked trjconv to produce a trajectory where nothing jumps through
one PBC boundary to another. So that means the total envelope of
coordinates must diffuse outward over time.

Mark

On Thu, Nov 3, 2016 at 3:27 PM Jan Riehm <
jriehm at bioinformatik.uni-saarland.de> wrote:

> Dear Gromacs-users,
>
> I've tried to center the atoms of the .trr file of my md simulation via
> trjconv -f traj.trr -o HCP_PRG_ALLFRAMES.pdb -s next.tpr -center -pbc
> nojump
> but it won't center all of them. I still got entries in my pdb like:
> ATOM     96  C   PRG B 411      44.401  -6.234  49.345  1.00 0.00
> ATOM     97  H   PRG B 411      44.050  83.757  47.724  1.00 0.00
> where the seconds row y-parameter is totally out of scale.
> So are there other ways to center my atoms?
> I've tried different groups for centering as well as different groups
> for outputs. There are slight changes in the coordinates, but overall
> the seen behaviour stays.
> So could they maybe be wrong in the trajectory file? Since i've
> accidently overwritten my original .trr file and renamed the backupfile
> for further usage
>
> Thank you very much,
> Jan
>
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