VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Mar 10 2011 - 08:18:03 CST

On Thu, Mar 10, 2011 at 7:36 AM, Taco de Wolff <tacodewolff_at_gmail.com> wrote:
> Hi,
> I hope this is the right place to ask.
>
> I wrote some conversion scripts for our MD simulations, the files are
> converted into the LAMMPS file format (and additionally a PSF file for the
> connectivity).
> This LAMMPSTRJ file contains all the atom positions as well as the PBC box
> boundaries.
>
> However, VMD does not show the box to be triclinic, eventhough I do define
> it to be as such.
>
> A simple file such as:
> ITEM: TIMESTEP
> 1
> ITEM: NUMBER OF ATOMS
> 1
> ITEM: BOX BOUNDS xy xz yz
> 0 6 0
> 0 6 3
> 0 6 0
> ITEM: ATOMS id mol type x y z
> 1 0 1 3 3 3
>
> Does _not_ show to be triclinic, eventhough by specification it should
> (shouldn't it?).
>
> After loading the lammpstrj data file, I show the box through the Tk
> Console, commanding 'pbc box'. The box is not skewed.
> I use VMD 1.8.7.
>
> Why is the box not shown triclinic? What is wrong?

your molfile plugin for lammps doesn't know about the extended
lammps trajectory format.
VMD 1.8.7 was released before LAMMPS supported triclinic cells.
VMD 1.9 will support reading triclinic cells from lammps trajectories
for regular (unscaled) coordinates. if you don't want to (why not?) or
cannot upgrade to VMD 1.9, you can download the sources for the
updated plugin and compilation instructions for linux machine here:
http://sites.google.com/site/akohlmey/software/lammps-icms
(the source archive is attached to the bottom of that page).

cheers,
   axel.

>
> Thank you,
> Taco
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.