|Date:||Thu, 05 Oct 2017 11:54:27 -0300|
I am having some trouble when converting a somewhat complex system from the packmol output to lammps data file using vmd.
I've seen Axel's tutorials, but I still could not produce an usable data file.
The system is a solid phase material composed by 2 different molecules inside a cube of 20x20x20. This cube goes inside a 40x40x40 cube where additional 1000 oxygen molecules are added. In the final system, there are 5 different elements.
So, I have the .pdb file for the final structure, but when converting to lammps data file and reading the vmd output, all atoms(elements) are changed.
Is there a way of avoiding this change? Or I'll have to do 4 different scripts in vmd (like the ones from Axel's tutorials) and try to assemble the system?