From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 10 2011 - 13:30:03 CDT

On Tue, May 10, 2011 at 1:56 PM, Haijun <huf11_at_psu.edu> wrote:
> Hi,
>
> I have a POSCAR file by VASP, I use VMD (1.8.7) to read it and then saved
> coordinates, choose POSCAR, then the coordinate changed strangely, which is
> not what I want, the structure is changed. Just read in and save out, I
> didn't do anything with the graph. I don't know whether it has something to
> do with the box. Does anybody have this problem. Thanks!!!

it is not a problem. it is a feature.

VMD cannot handle periodic display
of coordinates unless the unitcell is rotated
in a very specific orientation. most (classical)
MD codes generate trajectories according to
those conventions. however, most solid state
electronic structure codes use rotated unit cells
for computational efficiency.

in order to give you the best visualization,
most VMD plugins rotate your coordinates
according to the VMD requirements on reading.

if you read back the written out file, do you
get the same structure as before?
if yes, then this rotation is the cause,
if not, then there may be a bug in the
POSCAR writer. you'd have to contact the author,
since this is code that was contributed to VMD.

cheers,
     axel.

> My input POSCAR file by VASP:
> **************************************************************************
> pp                             4.09000000000000        2.8284271247461898
>  0.0000000000000000    0.0000000000000000
>    1.4142135623730949    2.4494897427831779    0.0000000000000000
>    0.0000000000000000    0.0000000000000000    8.0829037686547611
>  C    N    O      2     1     1   Selective dynamics
> Direct
>  0.3548963329056939  0.2386292361801097  0.4576784760662509   T   T   T
>  0.2131006946456214  0.2624310721160927  0.4527066803041102   T   T   T
>  0.3670230019904553  0.0336035425479118  0.4491527493994849   T   T   T
>  0.5638996343219198  0.0347274618276919  0.4372277282656143   T   T   T
> ****************************************************************************
>
>
> The output POSCAR file by VMD:
> ****************************************************************************
>
> C   N   O       1.000000000000
>    11.568266868591        0.000000000000        0.000000000000
>     5.784133434296       10.018414196966        0.000000000000
>     0.000000000000        0.000000000000       33.059078216553
> 2  1  1
> Direct
>     0.474210951223      -0.035156579115       0.457678469288
>     0.344316238791       0.063640024296       0.452706704719
>     0.383824777269      -0.187997768686       0.449152740883
>     0.581263370032      -0.300865059006       0.437227729353
> ****************************************************************************
>
> best,
>
> Hal
>

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