[gmx-users] unit cell vector warning
Tsjerk Wassenaar
tsjerkw at gmail.com
Wed Mar 23 16:49:14 CET 2016
Hi Irem,
The correction vectors is internal bookkeeping stuff, making sure to keep
track of what is where in a computationally efficient manner.
To get rid of this, I think the best option is to rotate your unit cell, to
have the largest vector (your third) along the x-axis. The second largest
should lie in the xy-plane, and the shortest vector (your first) should
have a positive z-component. This you can do with editconf -rotate. Gromacs
has some trouble with the third vector being the longest, while not
strictly perpendicular to the other two.
Hope it helps,
Tsjerk
On Wed, Mar 23, 2016 at 4:28 PM, Irem Altan <irem.altan at duke.edu> wrote:
> Hi,
>
> There’s been a small update on my unit cell problem. To recap the issue: I
> am trying to simulate a protein in its unit cell with water. The protein
> has the following unit cell dimensions: a=25.036, b= 29.410, c= 52.794,
> alpha= 89.45, beta= 86.29, gamma= 82.39. When I try to run energy
> minimization or an MD simulation, I get the following warning at every step:
>
> WARNING: Found more than 12 triclinic correction vectors, ignoring some.
> There is probably something wrong with your box.
> Box (3x3):
> Box[ 0]={ 5.00720e+00, 0.00000e+00, 0.00000e+00}
> Box[ 1]={ 7.78950e-01, 5.83019e+00, 0.00000e+00}
> Box[ 2]={ 6.83220e-01, 1.09700e-02, 1.05367e+01}
>
> This warning seems to go away if I change the angle alpha to 89.00 from
> 89.45. I’ve also tried doubling the unit cell sides, setting a=50.072,
> b=58.820, c=105.588. This has resulted in the same warnings as well. At
> this point, I’m wondering the following:
>
> 1- What does this warning mean? there doesn’t seem to be anything in the
> manual about this.
>
> 2- What are triclinic correction vectors?
>
> 3- Does it affect the simulation outcome? If so, how?
>
> 4- If it doesn’t affect the simulation, how can I suppress the warning?
> (If I don’t suppress it, it gets printed at every step, resulting in a very
> large output file (several gigabytes))
>
> Best,
> Irem
>
> > On Mar 8, 2016, at 11:38 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> >
> > 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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--
Tsjerk A. Wassenaar, Ph.D.
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