[gmx-users] box shape

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 4 19:39:52 CET 2010

mustafa bilsel wrote:
> Dear Lina,
> could you express these commands clearly? I am a new user!

You've been given commands that are almost exactly what you should enter in a 
terminal.  I would suggest you describe exactly why they aren't clear.

> editconf -f peptide.pdb/.gro -o peptide_center_in_simulation_
> box.gro -center x/2 y/2 z/2 -box x y z

The only comment I have here is that, for trivial centering within a box, 
neither -center nor -c is explicitly needed.  When defining a unit cell with 
either -box or -d, centering is implied.  Replace "x y z" with whatever box 
dimensions you want.

> genbox   -cp peptide_center_in_simulation_box.gro -cs spc216.gro -o 
> they_are_in_the_same_box_now.gro -p topol.top

This command can be used as is, replacing filenames as necessary.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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