[gmx-developers] pbc.c: put_atoms_in_triclinic_box

Berk Hess gmx3 at hotmail.com
Fri Dec 12 11:59:01 CET 2003

>The shift occurs in pymol as well as in rasmol. I don't know about the 
>other visualization packages. But in creating images, it can be a bit of a 

I understand.

But I just found out that there is another problem.
Gromacs default puts all atoms in a brick shaped volume.
For visualizing a protein simulation I think the most useful box shape
is the compact unitcell, for which the box edges unfortunately can
not be drawn by ngmx yet.
The problem now is that we can not just cange the box center, since
this produces a shift out of the box for the brick and compact 
Changing the center only for the triclinic representation also creates a 
since you would like to keep the center of the box constant over different
respresentations, otherwise your protein will not stay in the middle of the 


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