[gmx-users] Question about octahedral boxes

Justin A. Lemkul jalemkul at vt.edu
Mon Aug 4 20:35:13 CEST 2008

Hi everyone,

I'm having what seems to be an easily solvable problem, but I can't quite find 
the solution.  I have a very simple system - protein, water, and ions - in an 
octahedral box.  For visualization purposes, I would like to render the system 
in its true octahedral shape, but no matter what I do, I still get a rectangular 
box.  The threads in the archives have repeatedly stated that trjconv -ur 
compact solves this issue, but for me it is not working.  Maybe I'm making some 
silly mistake that I can't see, but I'd be very appreciative if someone could 
point it out.

editconf -f protein.pdb -d 1.0 -bt octahedron -o newbox.gro
(genbox and genion follow to give "solv_ions.gro")

Using the .tpr file I made for minimization:

trjconv -s min.tpr -f solv_ions.gro -ur compact -o compact.gro

Even with various iterations of -pbc, -center, and -boxcenter, I always get the 
same thing.  I have visualized my system in VMD, PyMOL, and ngmx, and everything 
shows the same shape.  My Gromacs version is 3.3.3, all tests passed after 
installation on my dual-core MacBook (OS X 10.5.4, gcc 4.0.1).

Any ideas?  Thanks for your attention.



Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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