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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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