Mod:Hunt Research Group/Chemshell:Chemshell: Visualising trajectories with VMD

Every time you run an optimisation with Chemshell a number of file will be crearted in the directory where the inputs are. Among these, the "path" files allow you to visualise the optimisation path of the system during the computation. First of all, you have to download the "path_active.xyz" file from the HPC down to your PC using the scp command in the bash. Now you can open VMD and simply drag the .xyz file in the Main window and the whole trajectory of the active region will be visible in the Display window. You can change the representation with the Graphics option in the tool bar and see the optimisation evolution by pressing play on the right corner of the main window.