I finally got my md running. I had to reduce my time step to avoid bond breakage. I have a couple of questions regarding trajectories. The cooordinates are between 0 and 1 while my box dimensions are -23 to 23 in each direction. What do those numbers mean and how do I transform them to my actual dimensions. I aslo need a procedure to make the trajectories to be viewed in VMD. It would be great if you cold forward me a detailed step to do this.
For dump style atom, the atom coords are normalized to 0 to 1. So a
value of 0.25 would mean (in your case) the atom is 1/4 of the way
between -23 and 23. You can change that with dump_modify.
Several dump formats can be read directly by VMD (xyz, xtc, dcd), Also
the native LAMMPS format I think. Or you can convert them using (for
example) the Pizza.py tool or other tools provided with LAMMPS.