Sometimes when you are animating a trajectory of a solvated system it can be helpful to be able to visualize the boundaries of the solvent box. The attached script allows you to do that.

PURPOSE: Reads in a trajectory from a simulation performed in a solvent box and creates a cell around the solvent box. The script modifies any existing cell parameters so that they represent the solvent box and the box can be displayed during animation. Note, the script does not automatically display the Cell/box in a line display. After running the script, make the Molecule Window Active and go to View >Display Style then click the Cell tab, choose Line or Stick and click OK. Then when you animate the trajectory the atoms should appear inside the box. Note, the initial molecule may not appear in the box but the conformations will.

INSTALLATION: Save DisplaySolvationCell.pl to a local directory or location accessible from the Files Explorer

USAGE: From DS Client: Open a file containing a solvent box trajectory. From the Files Explorer, double-click on the DisplaySolvationCell.pl to launch the script or right-click on the file and select Open With > Script Window then launch the script using the Run command from the Scripting toolbar. Once the script completes, make the Molecule window active, go to the View > Display Style command and click on the 'Cell' tab and change the Lattice Display to Line or Stick and optionally change the color then click OK.