[gmx-users] Trajectories not centered
jriehm at bioinformatik.uni-saarland.de
Thu Nov 3 15:27:17 CET 2016
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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