[gmx-users] bad box in protein.gro

[Alessandro Casoni]

Tsjerk Wassenaar ha scritto:
> Hi Alessandro,
>
> editconf encounters a bad box in the input file and I think it first
> replaces that with a standard box internally. Check the box at the end
> of box.gro to see if the result is what it should be (nine numbers,
> according to the specification of the rhombic dodecahedon in Chapter 3
> of the manual).
>
> Cheers,
>
> Tsjerk
>
> On 11/10/08, Alessandro Casoni <alessandro.casoni at unimi.it> wrote:
>   
>> Hi all,
>>  when i use "editconf" to generate a dodecahedron box with the command:
>>
>>  editconf -f protein.gro -bt dodecahedron -o box.gro -d 0.9
>>
>>  the output  show me the  following message:
>>
>>  .....
>>  WARNING 1 [file aminoacids.dat, line 1]:
>>   Bad box in file protein.gro
>>
>>  Generated a cubic box    6.941 x    4.939 x    7.460
>>  .....
>>
>>  what is the mean of "bad box in file"?
>>  and why editconf generates a cubic box?
>>
>>  I use gromacs 4.0
>>  regards,
>>  Alessandro
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>
>
>   
Thank you Tsjerk,

i appreciate your help..if i copy the last line at the end of box.gro in 
my protein.gro and rerun the editconf command i obtain:

Volume: 729.043 nm^3, corresponds to roughly 328000 electrons
No velocities found
    system size :  6.941  4.939  7.459 (nm)
    diameter    :  8.302               (nm)
    center      : -1.289 -0.528  4.099 (nm)
    box vectors : 10.102 10.102 10.102 (nm)
    box angles  :  60.00  60.00  90.00 (degrees)
    box volume  : 729.04               (nm^3)
    shift       :  8.866  8.105 -0.528 (nm)
new center      :  7.577  7.577  3.572 (nm)
new box vectors : 10.102 10.102 10.102 (nm)
new box angles  :  60.00  60.00  90.00 (degrees)
new box volume  : 729.04               (nm^3)

and the "bad box" message disappears..

Ale