VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Sep 19 2010 - 19:26:47 CDT

Hi,
  The C/C++ source code for the poscar plugin for VMD is attached
to this email. It was contributed by Sung Sakong, and only
a few bug fixes have been added here and there since his initial version.
I don't have any personal experience with VASP, nor do I have any
details on the minutiae of its file formats, so my only suggestion is
to have a look at the code and see if there are any assumptions being
made about the contents of the files, units, or other things that might
not be true in all cases. If you spot something, we can work with you
or Sung Sakong to get the associated VASP plugins for VMD fixed up.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Sep 14, 2010 at 03:36:00PM -0700, Tawhid Ezaz wrote:
> Hi,
> I am wondering how POSCAR plugin works in VMD.
> If I change the primitive lattice in POSCAR file, I am observing different
> atom positions in VMD than POSCAR files, even the coordinate system is
> cartesian. For example, if I try to shear a simulation box, thus changing
> both the premitive lattice and the coordinate of atoms to maintain
> periodicity, the atom positions shown in VMD are not same as POSCAR
> files.
> test1
> 4.646000
> 2.915565641232651 0 0.618795322093175
> 0.00000000000000 0.88420000000000 0.00000000000000
> -0.08440000000000 0.00000000000000 0.61880000000000
> 6 6
> Selective dynamics
> Cartesian(12)
> -0.05224154017060 0.00000000000000 0.07795577857023 T F F
> 0.60553242017061 0.44210000000000 0.02402246142977 T F F
> 0.863324101062050 0 0.696751100663409 T F F
> 1.521098061403250 0.442100000000000 0.642817783522949 T F F
> 1.863324101062040 0 0.696751100663409 T F F
> 2.521098061403250 0.442100000000000 0.642817783522949 T F F
> 0.00969365844125 0.44210000000000 0.41377554978375 T F F
> 0.45919722155874 0.00000000000000 0.30700269021625 T F F
> 0.925259299673910 0.442100000000000 1.032570871876928 T F F
> 1.374762862791390 0 0.925798012309428 T F F
> 1.925259299673910 0.442100000000000 1.032570871876928 T F F
> 2.374762862791400 0 0.925798012309428 T F F
> But if I shear the atom positions only, but not the premitive lattice,
> this will yield a right configuration in VMD (Periodicity will be affected
> though).
> test2
> 4.646000
> 3.00000000000000 0.00000000000000 0.000000000000000
> 0.00000000000000 0.88420000000000 0.00000000000000
> -0.08440000000000 0.00000000000000 0.61880000000000
> 6 6
> Selective dynamics
> Cartesian(12)
> -0.05224154017060 0.00000000000000 0.07795577857023 T F F
> 0.60553242017061 0.44210000000000 0.02402246142977 T F F
> 0.863324101062050 0 0.696751100663409 T F F
> 1.521098061403250 0.442100000000000 0.642817783522949 T F F
> 1.863324101062040 0 0.696751100663409 T F F
> 2.521098061403250 0.442100000000000 0.642817783522949 T F F
> 0.00969365844125 0.44210000000000 0.41377554978375 T F F
> 0.45919722155874 0.00000000000000 0.30700269021625 T F F
> 0.925259299673910 0.442100000000000 1.032570871876928 T F F
> 1.374762862791390 0 0.925798012309428 T F F
> 1.925259299673910 0.442100000000000 1.032570871876928 T F F
> 2.374762862791400 0 0.925798012309428 T F F
> I am wondering if you can help me what is going on in VMD calculations.
> thanks
> Tawhid 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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