[gmx-users] center of mass [question]

[David]

On Wed, 2004-07-14 at 19:55, Sergio Modesto Vechi wrote:
> 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?
Yes, within the accuracy of the file format. You can check by running it
again, it will print the current center.
> 
> Thanks in advance,
> 
> Sergio
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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