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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