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

[Tsjerk Wassenaar]

Hi David/Makoto,

I wouldn't call it a stupid error, keeping nine numbers for the
definition of a box. Of course in simulation the lower triangular part
of the box matrix is zero. But if you reorient the system and want to
preserve PBC (like after fitting), the box will be rotated and the
full matrix needs to be used to properly represent the system. Also,
in some cases (like the calculation of an optimal box shape based on
geometry), the initial orientation may not be aligned with the axes,
and the full representation (nine numbers) needs to be used, which can
then be transformed to a proper simulation cell for gromacs. The only
thing I find stupid are the messages "only triclinic boxes...[etc]"
and "box too skewed", since any box can be easily transformed to
comply with the rules for a proper box at any time.

Just my two cEUR.

Cheers,

Tsjerk

On Wed, May 7, 2008 at 8:33 AM, David van der Spoel
<spoel at xray.bmc.uu.se> wrote:
> 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
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623