[gmx-users] unit cell vector warning

[Irem Altan]

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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