[gmx-users] COM motion removal after simulation
martin.hoefling at gmx.de
Mon Dec 4 12:11:33 CET 2006
Is it possible to remove the COM movement of a protein after the simulation?
i tried it with trjconv but couldn't make it work:
trjconv -f traj.xtc -pbc cluster -s topol.tpr -n index.ndx -o
trajout.xtc -center rect
I select "Protein" for clustering and centering and "System" for output.
com seems to change nothing. Clustering keeps the protein consistent but not
in the middle of the box.
All I could find with a quick search is about com removal during simulations.
I can hook a routine for each frame via trajconv but this seems ugly to me,
maybe someone here knows a smoother way.
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