[gmx-users] unit cell vector warning

[Irem Altan]

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