# [gmx-users] Re: Hexagonal prism

Simon Wang sim_wang03 at hotmail.com
Fri Feb 20 05:13:01 CET 2004

```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.

Thanks,

Simon

>From: David van der Spoel <spoel at xray.bmc.uu.se>
>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>
> >>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.

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