[gmx-users] g_density and g_potential for DMPC bilayer
agu at fyslab.hut.fi
Mon Jun 23 17:49:01 CEST 2003
> I don't see where the problem is. You give your trajectory to trjconv
> trjconv -f traj.xtc -n index.ndx -o trajout.xtc
> because you specify an index, the program asks you the group you
> want to center and the group you want as output. So as output you
> have your whole system centered on the group you choose. The center
> the program chooses is probably geometrical but check on some snapshots
> you'll find that it is almost the same as the COM. It would be necessary
> to check the code but I am also convinced that the program re-centers
> in the box at each frame of the trajectory.
Well, if trjconv re-centers at each frame, this solves the problem, of
> As for the program to get the PN orientation no problem. I'll send you a
> copy later today.
Thanks a lot for your help!
Dr. A. Gurtovenko
Biophysics and Soft Matter Group
Laboratory of Physics
Helsinki University of Technology
e-mail: agu at fyslab.hut.fi
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