This page is a work in progress, and will be updated as I figure out more ways to use NAMD Energy.

Getting started

You'll need to do file conversions out of GROMACS file types before you can use NAMD energy. Follow the instructions for using gRINN to get .pdb, .psf, and .dcd files.

Setting up

1. Open VMD and load the .pdb, .psf. and .dcd files (in that order) by going to File > New Molecule.

2. On the main VMD window, click Extensions > Analysis > NAMD Energy.

3. If you have more than one molecule (.pdb, .gro) file open, make sure the correct one is selected.

4. Enter your selections into the appropriate boxes. For example, if you're trying to calculate overall interaction energy between two chains (as you'll need to do on the Mutations List spreadsheet), type chain A into selection 1 and chain B into selection 2.

5. Select the appropriate energy type. Often, you'll be interested in VdW (Van der Waals, the small random interactions between all atoms) and Elec (electrostatic energy, including hydrogen bonding). If you need other energy types, feel free to select those as well.

6. If you want to keep the data and analyze it more thoroughly (usually when you're not doing residue-by-residue analysis), name the output file, but do not give it an extension. I recommend naming it something like complex-name-energy, as appropriate for your simulation.

7. Specify the parameter file. We usually use this one. You may need to change the file type to all files in the selection window, since VMD doesn't recognize it.

8. Click the run button. You will probably need to specify the location of your NAMD executable, so do that when prompted – you're looking for the namd2 file.

Reading the results

NAMD Energy will spit out a table (whatever you named it!) that can be read with a text editor. However, to analyze this data any way other than visually, we have to get a little creative.

1. Open the file in a text editor (on Mac, this is TextEdit; on Windows, this is Notepad; on Linux, this could be anything – I use gedit).

2. Manually add commas immediately following everything. This is tedious, but if you get your rhythm down with your comma button and your arrow keys, it goes faster than you think. Don't put commas after anything in the last column, but do put a comma after every "cell". I promise, this is necessary.

3. Earlier, you didn't put a file extension (.txt, .xls, etc.) after the file name. Now, you're going to add one. Either do a Save As or rename the file (depending on your system) and put .csv at the end of the file name. If you're doing a Save As, make sure you choose All Files instead of .txt or similar.

4. Open the file with your spreadsheet software. I use Excel, but if you don't have that, Numbers, LibreOffice, or uploading it to Google Sheets should do fine.

5. Now, you can do more complex numerical analysis. You can select all the numbers in a column and you should be able to see the average at the bottom. Don't include the first row of numbers (frame 0) since it's identical to frame 1. On Google Sheets, click the Sum or Count dropdown to read the average. You'll need this information for the Mutations List.

6. You can manipulate this data however else you want once it's in a .csv format. Make sure you upload a clean version to the Drive and link it on the Mutations List sheet, if you're doing this for a designed decoy.