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

[David van der Spoel]

Makoto Yoneya wrote:
> 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
Hi Makoto,

three of these values are always zero, so there really are only six 
variables as it should be. This is due to some stupid error 15 years ago 
and now we have to be backwards compatible with our old gro files.
You can just try it with a pdb file that has a = b = c = 1 and alpha 
beta gamma as you like it.

> 
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se