[gmx-users] Simulation Box

Tsjerk Wassenaar t.a.wassenaar at chem.rug.nl
Mon Jul 19 15:52:34 CEST 2004

Hi Hadas,

Really, there is no box in Gromacs output. There are lattice vectors 
which you can use to define a simulation box anywhere and in whichever 
way you want. It's perfectly okay to take the origin as one extreme of 
the box and use the lattice vectors to construct a triclinic, but you 
might as well use them to construct a general rhombic dodecahedron or 
any other type of box around the origin.
If it is for visualisation matters you can use  trjconv -pbc inbox | 
compact to put them in the box vor viewing.



Hadas Lapid wrote:

> I wanted to know weather on the output .gro (/ .pdb) trajectory file 
> the boundary corner of the simulation box is located conventionally at 
> (0,0,0) coordinates.
> and if not, how can I find the coordinates of the box (its boundaries) 
> without having to sort the molecular coordinates of all atoms in 
> search for extremal values of x,y and z in each frame?
> Sincerely,
> Hadas
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