[gmx-developers] WARNING: Found more than 12 triclinic correction vectors, ignoring some.

[Justin A. Lemkul]

Hi all,

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

-- 
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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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