[gmx-users] box vectors entry in "gro" file

[Makoto Yoneya]

Dear GROMACS users:

I found the following in ML archive about the box vectors entry in "gro"
file.

>> doing:
>> % editconf -f <in.pdb> -o <out.gro> -bf tric -box a b c -angles bc ac 
>> ab
>> 
>> the last line of out.gro looks like:
>>    1.12020 0.92620 6.259008 0.00000 0.00000 0.00000 0.00000 -0.99134 
>> 0.00000
>> 
>> what are these 9 values in this case? (angles, unit cell vectors..) why
nine?
>
>They are the XX YY ZZ XY XZ YX YZ ZX ZY components of the three box 
>vectors. The ordering is a bit counterintuitive, but that is because it 
>keeps the XX YY ZZ 'cubic' part of the box vectors in the beginning, so 
>it corresponds to the case where only the three box-edge lengths are 
>defined for a cubic box.

Could someone kindly teach me the exact translate formulas from PDB file
CRYST1 
entry of "a, b, c, alpha, beta, gamma"
to the gro file entry "XX YY ZZ XY XZ YX YZ ZX ZY" above?

Thank you for advance.

Makoto Yoneya, Dr.
AIST, Japan