[gmx-users] unit cell vector warning

[Mark Abraham]

Hi,

How are you actually generating the coordinate file, and/or the box
vectors? As far as I know, nobody's written down the set of vectors that
should work sensibly, but it's likely that the gmx tools will write boxes
that will definitely work later on...

Mark

On Tue, Mar 8, 2016 at 4:27 PM Irem Altan <irem.altan at duke.edu> wrote:

> Hi,
>
> An update on the unit cell problem: when I make small changes in the
> angle, say change 89.45 to 89.00, the error disappears. I’m still getting
> the same warning. This is with version 5.1.2. Could this be a numerical
> precision issue (c_y is 0.05, see below) or a bug? I tried to run this
> without the protein, by just putting water and a few ions in the box.
>
> Best,
> Irem
>
> > On Mar 3, 2016, at 4:15 PM, Irem Altan <irem.altan at duke.edu> wrote:
> >
> > Hi,
> >
> > I am trying to simulate a protein in its triclinic unit cell. During the
> energy minimization and MD simulation, GROMACS prints the following out at
> every step:
> >
> > WARNING: Found more than 12 triclinic correction vectors, ignoring some.
> >  There is probably something wrong with your box.
> > 0.00000e+00,  0.00000e+00}
> >  3.89470e-01,   2.50360e+00  3.41610e-01          Box[    1]={
> 3.41610e-01,  5.49000e-03,  5.26833e+00}
> > 2.91510e+00         Box (3x3):
> > 2.91510e+00, ,  0.00000e+00}
> >            Box[    1]={         Box[    0]={ 0.00000e+00 2.50360e+00
> 5.49000e-03,
> >
> > I checked the .gro file to see the unit cell vectors are listed
> correctly.
> >
> > The protein has the following sides and angles:
> >
> > a = 25.04, b = 29.41, c = 52.79, α = 89.45, β = 86.29, γ = 82.39
> >
> > and I calculate the unit vectors to be:
> >
> > a = [ 25.036,   0.   ,   0.   ]
> > b = [  3.8947483 ,  29.15096972,   0.        ]
> > c = [  3.41611372,   0.05486764,  52.68333316]
> >
> > and the .gro file has the line:
> >
> >   2.50360   2.91510   5.26833   0.00000   0.00000   0.38947   0.00000
>  0.34161   0.00549
> >
> > which seems to be correct.
> >
> > I have also verified that the conditions 3.1-3.3 listed on page 12 on
> the manual for 5.1 to be correct.
> >
> > What could be the problem?
> >
> > Best,
> > Irem
> > --
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