[gmx-users] Re: Hexagonal prism

[David]

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) ?

you are not expecting crystal symmetry, are you? 

> 
> Thanks,
> 
> Simon
> 
> >From: David van der Spoel <spoel at xray.bmc.uu.se>
> >Reply-To: gmx-users at gromacs.org
> >To: gmx-users at gromacs.org
> >Subject: Re: [gmx-users] Re: [gmx-developers] Hexagonal prism
> >Date: Thu, 19 Feb 2004 13:29:26 +0100 (CET)
> >
> >On Wed, 18 Feb 2004, Simon Wang wrote:
> >
> > >Hi, GMX users:
> > >
> > >I got a little bit confused about how to define a hexagonal unit cell as 
> >a
> > >special case of triclinic cell. When using "editconf -f conf.gro -o 
> >out.gro
> > >-bt tric -box 5 5 3 -angles 90 90 120 -c" to assign the values of a, b, 
> >c,
> > ><bc, <ac, <ab, followed by conversion of "trjconv -pbc inbox -ur compact" 
> >or
> > >"trjconv -pbc whole -ur compact", I can get the right shape of hexagonal
> > >prism. But the SIZE of the hexagonal edge is about 30 angstrom, not 50 as
> > >defined. I guess I don't fully understand the way GROMACS define the
> > >triclinic cell. I hope someone can help me out.
> >
> >manual chpater 3
> >  (with figures)
> > >
> > >Thanks,
> > >
> > >Simon
> > >
> > >>From: David van der Spoel <spoel at xray.bmc.uu.se>
> > >>Reply-To: gmx-users at gromacs.org
> > >>To: Simon Wang <sim_wang03 at hotmail.com>
> > >>CC: gmx-users at gromacs.org
> > >>Subject: [gmx-users] Re: [gmx-developers] Hexagonal prism
> > >>Date: Wed, 18 Feb 2004 11:25:59 +0100 (CET)
> > >>
> > >>On Tue, 17 Feb 2004, Simon Wang wrote:
> > >>
> > >> >Hi, David:
> > >> >
> > >> >I've installed GROMACS 3.2.0 and tried the new version of trjconv.
> > >> >Unfortunately I still could not get the right size of hexagonal prism. 
> >I
> > >> >tried the following things:
> > >> >trjconv -pbc whole -ur compact
> > >> >trjconv -pbc com -ur compact
> > >> >
> > >> >However, there is no option like "compact" for -pbc. If this is a bug, 
> >do
> > >> >you ever have plan to fix it in the near future?
> > >>
> > >>it's not necessary.
> > >>
> > >>trjconv -pbc inbox -ur compact does what you want.
> > >>
> > >>please put further questions to the mailing list only.
> > >> >
> > >>
> > >>--
> > >>David.
> 
> _________________________________________________________________
> Get fast, reliable access with MSN 9 Dial-up. Click here for Special Offer! 
> http://click.atdmt.com/AVE/go/onm00200361ave/direct/01/
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++