Hi all,
I tried to send this to the gmx-developers list several hours ago, but it never
showed up, so I'll try here. There also appears to be problems with the Admin
pages for the mailing lists (I went to check and make sure my subscription to
that list was active).
I am simulating a simple protein/ligand in water using an octahedral box. For
visualization purposes, I am rendering the box in its true octahedral shape
using the following command:
trjconv -s md.tpr -f 20ns.xtc -o compact.xtc -ur compact -pbc mol
When I do this, I receive a series of warnings like the following:
WARNING: Found more than 12 triclinic correction vectors, ignoring some.
There is probably something wrong with your box.
Box (3x3):
Box[ 0]={ 6.87729e+00, 0.00000e+00, 0.00000e+00}
Box[ 1]={ 3.23209e+00, 6.46199e+00, 0.00000e+00}
Box[ 2]={-2.97018e-01, 1.10216e-03, 5.59953e+00}
I saw a previous discussion across the list here:
http://www.gromacs.org/pipermail/gmx-developers/2006-November/001953.html
The result was a request for a bugzilla and a potential fix. I am using GMX
3.3.3, and the warnings only seem to come up when I use -pbc mol. Other PBC
corrections (like nojump) don't seem to result in these warnings.
When I visualize the trajectory, the box seems to smoothly morph between an
octahedron and a rectangular shape. I don't know if that's relevant or just a
consequence of visualization.
Any ideas as to what's going on? Is there a problem with this type of
manipulation?
Thanks in advance for any comments.
-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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