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