[gmx-users] Re: Hexagonal prism
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>
> >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
> > > the conventional unit cell parameters, in the case of a hexagonal prism
> > > tric -box 5 5 3 -angles 90 90 120), the box volume should be 194.86
> > > However, editconf report the volume as 64.95 nm^3, one third of the
> > > one. So I guess the box vector is not the same as the conventional unit
> > > 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
> > > 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 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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