[gmx-users] COM motion removal after simulation

Martin Höfling martin.hoefling at gmx.de
Mon Dec 4 12:11:33 CET 2006

Hi all,

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.

Any hints?

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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