[gmx-users] g_density and g_potential for DMPC bilayer

[Andrei Gurtovenko]

>
> 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 
course.


>
>
> As for the program to get the PN orientation no problem. I'll send you a
> copy later today.

>
>
> Xavier
>
Thanks a lot for your help!


Andrei

-- 
Dr. A. Gurtovenko

Biophysics and Soft Matter Group
Laboratory of Physics
Helsinki University of Technology
P.O.Box 1100
FIN-02015 HUT
Finland
Tel.: +358-9-4515803
e-mail: agu at fyslab.hut.fi