VMD-L Mailing List

From: Eduard Schreiner (eduard.schreiner_at_theochem.ruhr-uni-bochum.de)
Date: Fri Mar 11 2005 - 13:02:50 CST

Andre Farias de Moura wrote:
> Hi all,
>
> I've performed a simulation using anisotropic pressure coupling
> in GROMACS and I'd like to draw the edges of the box along with
> the molecules, but I don't know how to convert the box dimensions
> given at the bottom of the gro file into the set of positions
> that I should supply to the draw command:
>
> draw line {x1 y1 z1} {x2 y2 z2}
>
> the figures at the gro file are something like:
>
> 7.41837 4.97798 9.68571 0.00000 0.00000 1.07660 0.00000
> 2.60859 -1.47440
>
> I know these numbers fully describe the box size and shape, I guess
> they are named as xx, yy, zz, xy, yx, xz, zx, yz, zy.
>
> the question is: how can I convert these 9 numbers into a set of
> 8 vertices coordinates defining the 3D polygon I'm after?
>
> thanks in advance,
>
> andre'
>
> /-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
>
> Dr. Andre' Farias de Moura
>
> /-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
>
> Laboratorio de Quimica Teorica
> Universidade Federal de Sao Carlos
> Sao Carlos - SP - Brasil
>
> /-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
>
> Endereco Atual
>
> Grupo de Quimica Quantica
> Instituto de Quimica de Sao Carlos
> Universidade de Sao Paulo
> Sao Carlos - SP - Brasil
> Telefone: 55-16-3373-8055
>
> /-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
>
>
>
Hey Andre',
if vmd reads the information of the box dimensions (I am not sure, but I
think it does), You could try :

draw unitcell

Check:

http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part7.html#chap9_sect1

section: "9.1. Collected 'draw' Extensions"

I hope this helps You.

Eduard Schreiner 

-- 
--
=======================================================================
Eduard Schreiner                        e-mail: eduard.schreiner_at_rub.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-22121
Ruhr-Universitaet Bochum - NC 03/52         Fax:   ++49 (0)234/32-14045
D-44780 Bochum                               http://www.theochem.rub.de
=======================================================================