Molecular Dynamic visualisation using VMD

.vmdrc

# light controlling
# turn on lights 0 and 1
light 0 on
light 1 on
light 2 off
light 3 off

# position the stage and axes
axes location off
stage location off

# turn on menu windows
menu main on
menu graphics on
menu files on

# position menu windows
menu main move 5 600
menu files move 800 50 
menu graphics move 613 139 

# set initial drawing method to points
mol modstyle 0 0 points 10

# draw a box around the periodic unit cell boundaries
proc box_molecule {molid} {
      # get the min and max values for each of the directions
      # (I'm not sure if this is the best way ... )
      set sel [atomselect top all]

      set coords [lsort -real [$sel get x]]
      set minx [lindex $coords 0]
      set maxx [lindex [lsort -real -decreasing $coords] 0]

      set coords [lsort -real [$sel get y]]
      set miny [lindex $coords 0]
      set maxy [lindex [lsort -real -decreasing $coords] 0]

      set coords [lsort -real [$sel get z]]
      set minz [lindex $coords 0]
      set maxz [lindex [lsort -real -decreasing $coords] 0]

      # and draw the lines
      draw materials off
      draw color yellow
      draw line "$minx $miny $minz" "$maxx $miny $minz"
      draw line "$minx $miny $minz" "$minx $maxy $minz"
      draw line "$minx $miny $minz" "$minx $miny $maxz"

      draw line "$maxx $miny $minz" "$maxx $maxy $minz"
      draw line "$maxx $miny $minz" "$maxx $miny $maxz"

      draw line "$minx $maxy $minz" "$maxx $maxy $minz"
      draw line "$minx $maxy $minz" "$minx $maxy $maxz"

      draw line "$minx $miny $maxz" "$maxx $miny $maxz"
      draw line "$minx $miny $maxz" "$minx $maxy $maxz"

      draw line "$maxx $maxy $maxz" "$maxx $maxy $minz"
      draw line "$maxx $maxy $maxz" "$minx $maxy $maxz"
      draw line "$maxx $maxy $maxz" "$maxx $miny $maxz"
}

# draw the box
box_molecule top