[gmx-users] Re: Hexagonal prism

[Simon Wang]

>From: David <spoel at xray.bmc.uu.se>
>Reply-To: gmx-users at gromacs.org
>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 :(

>
>you are not expecting crystal symmetry, are you?
>

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