[gmx-users] Trajectories not centered

Jan Riehm jriehm at bioinformatik.uni-saarland.de
Thu Nov 3 15:27:17 CET 2016

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,

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