# [gmx-users] Re: Hexagonal prism

David spoel at xray.bmc.uu.se
Sat Feb 21 09:50:02 CET 2004

```On Sat, 2004-02-21 at 03:49, Simon Wang wrote:
> >From: David <spoel at xray.bmc.uu.se>
> >To: gmx-users at gromacs.org
> >Subject: Re: [gmx-users] Re: Hexagonal prism
> >Date: Fri, 20 Feb 2004 16:15:31 +0100
> >
> >On Fri, 2004-02-20 at 05:11, Simon Wang wrote:
> > > Hi, GMX users:
> > >
> > > One more question. If the box vector and angles used in GMX are the same
> >as
> > > the conventional unit cell parameters, in the case of a hexagonal prism
> >(-bt
> > > tric -box 5 5 3 -angles 90 90 120), the box volume should be 194.86
> >nm^3.
> > > However, editconf report the volume as 64.95 nm^3, one third of the
> >previous
> > > one. So I guess the box vector is not the same as the conventional unit
> >cell
> > > parameters. But if GMX convert the hexagonal prism structure file to PDB
> > > format, the box vectors show up at CRYST1 line as the unit cell
> >parameters.
> > > I hope someone can help me out.
> >
> >shouldn't it be 5 x 5 x 3 sin (120) ?
>
> If you divide the hexagonal prism (-bt tric -box 5 5 3 -angles 90 90 120)
> into three equal monoclinic cell, each monoclinic cell has the volume of 5 x
> 5 x 3 sin (120). That't the reason why the hexagonal prism I got from
> GROMACS is one third smaller than the one I defined :(

It can be done however, you just have to redefine your unit cell as a P1
cell. Gromacs cannot handle crystallographic symmetry, so you need to
simulate an entire unit cell.
>
> >
> >you are not expecting crystal symmetry, are you?
> >
>
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--
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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