VMD-L Mailing List
From: Taco de Wolff (tacodewolff_at_gmail.com)
Date: Thu Mar 10 2011 - 06:36:22 CST
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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?
Thank you,
Taco
- Next message: Olaf Lenz: "Re: Zero box vector"
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- Next in thread: Olaf Lenz: "Re: Triclinic boxes in VMD using the LAMMPS file format"
- Reply: Olaf Lenz: "Re: Triclinic boxes in VMD using the LAMMPS file format"
- Reply: Axel Kohlmeyer: "Re: Triclinic boxes in VMD using the LAMMPS file format"
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