VMD-L Mailing List

From: Tawhid Ezaz (ezaztaw_at_yahoo.com)
Date: Tue Sep 14 2010 - 17:36:00 CDT

 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