[gmx-developers] Hexagonal prism

[David van der Spoel]

On Mon, 2004-02-16 at 12:56, Anton Feenstra wrote:
> David wrote:
> 
> > On Sat, 2004-02-14 at 00:04, Simon Wang wrote:
> > 
> >>Hi, all:
> >>
> >>I am trying to build a hexagonal prism box via the definition of a triclinic 
> >>box in GROMACS 3.0.5:
> >>editconf -f conf.gro -o out.gro -bt tric -box 5 5 3 -angles 90 90 120 -c
> >>
> >>Then I genbox the box with SPC waters. After " trjconv -pbc whole -ur 
> >>compact" to convert to the viewable format, I checked the size the triclinic 
> >>box. However, the edge of the hexagonal prism is not 5 as I defined at the 
> >>begining. I was wondering if it is a unresolved bug.
> >>
> > 
> > maybe. upgrade to 3.2, here I get a box of:
> >    5.00000   4.33013   3.00000   0.00000   0.00000  -2.50000   0.00000 
>                 ^^^^^^^
> 
> That is not 5!
No, but 4.33013^2 + 2.5^2 = 5^2


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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