[gmx-users] center of mass [question]
spoel at xray.bmc.uu.se
Wed Jul 14 20:54:51 CEST 2004
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,
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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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