[gmx-users] Re: [gmx-developers] Hexagonal prism

Simon Wang sim_wang03 at hotmail.com
Thu Feb 19 04:12:00 CET 2004

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.



>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.
> >

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