VMD-L Mailing List

From: Haijun (huf11_at_psu.edu)
Date: Tue May 10 2011 - 12:56:09 CDT

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!!!

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