[gmx-users] center of mass [question]

Sergio Modesto Vechi smv at glu.fcfrp.usp.br
Wed Jul 14 19:55:18 CEST 2004

Dear Gmx-ers,

I have obtained a trajectory file of a protein, 2 Ca2+ ions, 3 Na+ ions 
and water molecules. 
Before the simulation,  the box was modified with editconf command to 
center the protein
in the box:
editconf -bt cubic -box 5.71 5.71 5.71 -center 2.855 2.855 2.855 -d 1.2
Now I have extracted some pdb frames from my trajectory and wrote only 
the coordinates
of the protein and the Ca2+ ions using an index file and the trjconv 
command. Then I used
editconf to center the system in (0.0, 0.0, 0.0) do to some calculations:
editconf -center 0.000 0.000 0.000 -f frame.pdb -o frame_new.pdb

My question is: when I used editconf to center my system (protein and 
ions Ca2+) in zero,
Do I guarantee that the zero is the center of mass of this system? If 
not how can I do this?

Thanks in advance,


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