Using VMD to extend cell

Build a following file script.tcl. And run vmd -e script.tcl.

You may change the input PRMTOP and DCD to PDB or XYZ, and the output 1.dcd to PDB or XYZ according to your condition. The instruction can be found at http://www.ks.uiuc.edu/Research/vmd/current/ug/node140.html.
The fourth line is about how to extend the original cell. “1 2 1” means to extend 1 more cell at y direction. If you change it to “2 1 1“, it means the cell would extend to x direction 1 more cell. So you may extend the cell to a super big cell.

package require topotools
set mol [mol new Your_molecule.prmtop waitfor all] 
mol addfile Your_trajectory.dcd first 0 last 0 
set newmol [::TopoTools::replicatemol $mol 1 2 1 ]
animate write dcd 1.dcd $newmol
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