[gmx-users] Re: Question about octahedral boxes (solved)

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 5 03:31:54 CEST 2008

Just to follow up to my own message - I have solved this problem.  Based on some 
archived materials from the Stanford workshop on the wiki site, I have 
successfully re-generated the correct octahedral representation with the following:

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

Somehow I had overlooked trying -pbc mol in my earlier attempts.


Justin A. Lemkul wrote:
> 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


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


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