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

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Nov 21 17:01:15 CET 2006

Hi Berk,

No, I'm not using CVS code. But I was not aware of this requirement,
which is not mentioned in the manual. There it's stated (equation 3.3)
that neither |box[1][x]| nor |box[2][x]| should be larger than
box[0][x]/2. It doesn't mention the combination. Also, although it is
always possible to transform the box to meet the requirements
mentioned in the manual, I believe this is not so for the requirement
you mention. That would mean that certain lattice arrangements are
thus forbidden in Gromacs. Or am I missing something?

What is the consequence of having more than 12 correction vectors? I
presume they are used to short cut determination of minimal distances.
So, with more correction vectors, this may be slower in some cases? It
seems not to affect the simulation in any case.


On 11/21/06, Berk Hess <hessb at mpip-mainz.mpg.de> wrote:
> Tsjerk Wassenaar wrote:
> > Hi,
> >
> > I met the following warning when running genion:
> >
> > WARNING: Found more than 12 triclinic correction vectors, ignoring some.
> >  There is probably something wrong with your box.
> >         Box (3x3):
> >            Box[    0]={ 6.79189e+00,  0.00000e+00,  0.00000e+00}
> >            Box[    1]={-2.06669e+00,  5.07661e+00,  0.00000e+00}
> >            Box[    2]={ 1.33585e+00, -1.79879e+00,  4.65595e+00}
> >
> > This is strange, since the box fully complies with the gromacs rules
> > (it was transformed to comply with gromacs rules). I tracked the
> > message to low_set_pbc in pbc.c, but couldn't figure out the rationale
> > behind the warning. Maybe one of the developers could shed some light
> > on the matter? To my opinion, gromacs shouldn't complain/warn about a
> > box meeting its standards. Also, editconf/genbox did not complain.
> >
> Your box does not really comply with the Gromacs requirements.
> (-box[1][x]+box[2][x])/box[0][x] = 0.50097
> This is more than 0.5, so there are more than 12 correction vectors.
> There is a small margin in correcting the box vectors in Gromacs,
> so we do not continuously change them because of rounding issues.
> But the margin was always 0.5001. In CVS it is currently 0.501.
> So are you using CVS code?
> Berk.
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Tsjerk A. Wassenaar, Ph.D.
NMR, Utrecht University,
Padualaan 8,
3584 CH Utrecht, the Netherlands
P: +31-30-2539931
F: +31-30-2537623

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