Loading a trajectory

1. On the VMD main window, go to File → New Molecule
2. The "Molecule File Browser" window will appear. Under the "Load Files for:" list box, select "New Molecule"
3. Click "Browse…"
4. Navigate to "…/cpaf.prmtop" Click "OK"
5. In the Molecule File Browser, click "Load"
6. Under the "Load Files for:" list box, select "cpaf.prmtop"
7. Click "Browse…"
8. Navigate to "…/cpaf.dcd" Click "OK". The trajectory will begin to load

Align the molecule

1. In the VMD Main window, select Extensions → Analysis → RMSD Trajectory Tool. The RMSD Trajectory window will appear.
2. Make sure the text in the top left corner says "protein"
3. Below that, select the "Backbone" checkbox
4. Make sure the checkbox labelled "Trajectory" is selected, with Frame ref set to "0"
5. Click the "Align" button to align every frame of the protein to the first frame.
6. Close the RMSD Trajectory Tool Window.

Start the Delphi run

1. In the VMD Main window, select Extensions → Analysis → DelEnsembleElec. The DelEnsembleElec plugin window will appear.
2. Under the option box "Select molecule for Delphi run:" select "1:cpaf.prmtop"
3. In the "Selection" textbox, leave the value at "protein"
4. In the "Write to Output" textbox, change the value to "traj_cpaf.cube"
5. Deselect the "Load into VMD when finished" option, and instead select "Load first frame colored by charge".
6. Go to the menubar "Edit" → "Input File". The Edit Delphi Input File window will appear.
7. Click the button "Load Template Param. File"
8. Navigate to the file "…/param.in". Click "Open"
9. As before, the "Size File" and "Charge File" fields must point to the proper .siz and .crg parameter files that came with your Delphi package or may be downloaded at Clemson's Website.
10. Click "OK" to close the Edit Delphi Input File window
    Note: The trajectory provided in this tutorial has 100 frames, so the entire run will probably take 100 times longer than the single frame calculation done in the previous section: potentially amounting to hours or days. The results of a completed run of this tutorial's trajectory has been provided in the tutorial files.

11. click the "Run Delphi" button.

11. In the VMD main window, go to: File → New Molecule
12. The "Molecule File Browser" window will appear. Under the "Load Files for:" list box, select "0: cpaf.prmtop"
13. Click "Browse…"
14. Navigate to "…/cpaf_traj_example.cube" Click OK
15. In the Molecule File Browser, click "Load"
16. In the VMD Representations window, under the "Drawing method" tab, select "surf"
17. In the VMD Representations window, under the "Coloring method" tab, select "volume"
18. Zoom out your view so you can see the whole molecule.

Examine the results

1. The color differences are very faint. To fix that, go to the Trajectory tab in the Graphical Representations window.
2. Change the values in the two "Color Scale Data Range" boxes to numbers closer to zero. -/+10 should suffice for this case.