[gmx-users] unit cell vector warning

[Irem Altan]

Hi,

I'm generating the box from the.pdb file with pdb2gmx. The protein in question is 5e1k. I do the simulations in the protein unit cell. 

Best,
Irem

> On Mar 8, 2016, at 11:39 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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