I am using ASE to write an
xyz file. Each frame in the file has a different PBC (periodic boundary condition). Currently, a frame starts like this:
192 Lattice="23.46511 0.0 0.0 0.0 23.46511 0.0 0.0 0.0 23.46511" Properties=species:S:1:pos:R:3:force:R:3 TotEnergy=-1103.24236 cutoff=-1.0 nneightol=1.2 pbc="T T T" O 11.72590000 14.59020000 1.86929000 -0.04213780 0.03788820 0.00314949 H 12.69400000 16.13880000 1.25499000 -0.03709700 -0.03453660 0.01566490
The lattice coordinates are what I want to use as the PBC box. However, when I try to visualize this file in VMD, it throws the following error and doesn't show the box:
vmd > pbc box ERROR) Suspicious pbc side length (a=0.000000 b=0.000000 c=0.000000). Have you forgotten to set the pbc parameters?
What should be done to include
c in the
xyz file so that it is compatible with
pbc box in VMD?