[gmx-users] g_density and g_potential for DMPC bilayer

[David]

On Mon, 2003-06-23 at 17:48, Andrei Gurtovenko wrote:
> >
> > 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.
trjconv -h
 -[no]center   bool     no  Center atoms in box
 


> 
> 
> >
> >
> > 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
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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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