Running a simulation with AutoIMD

Here, we describe a VMD extension called AutoIMD (where IMD stands for Interactive Molecular Dynamics). The purpose of this tool is to automatically setup a NAMD simulation that can be visualized in real-time in VMD. AutoIMD takes care of generating all the necessary files (PDB/PSF/NAMD config) and of launching and connecting to a NAMD simulation. Once you have connected VMD to a running simulation, you can see your molecule's motion as it is being computed!

1. In VMD and in the nanotubes working directory, load the files imdnanotube.psf and imdnanotube.pdb into a new molecule.

2. Create a new representation for the molecule in VMD. Select only atoms of the nanotube for the new representation by typing carbon into the atom selection window. Choose the Charge Coloring Method. This will display different charges using different colors.

To get started with AutoIMD, follow these steps:

3. Open the AutoIMD window through the VMD Extensions $\rightarrow$Simulation $\rightarrow$AutoIMD menu item.

4. In the AutoIMD window, select the Settings $\rightarrow$ Simulation Parameters... menu item. A new window should pop up (Fig. 3). In this new window, completely erase the contents of the text input field named CHARMM Params, and then click on the Add... button. You will now need to locate the CHARMM parameter file called par_nanotubes.inp in the nanotubes working directory and click on Open. When you have specified the right parameter file, you can dismiss the Simulation Parameters window (by clicking on its close box).

Figure 3: The AutoIMD Simulation Parameters dialog.

AutoIMD allows you to specify a region of your molecule that you wish to simulate. To do this, it separates the molecule into three regions: a molten region, a fixed region and an excluded region. The molten region is the one that will be moving in the simulation. To hold the molten region in place, AutoIMD finds all the atoms that surround it (this is the fixed region) and uses them as unmoving constraints for the molten region. Atoms that are very far from the molten region are not simulated in order to make the simulation faster; they constitute the excluded region.

5. In the AutoIMD window, in the molten selection text input box, enter same residue as water and (x*x + y*y < 16) . This corresponds to the cylinder of water of radius 4 Å that we wish to simulate. The other atoms will become part of the ``fixed" region.

6. Then, choose Local from the next menu in the window. This will make the simulation run on your local machine. After these steps, your AutoIMD window should look like Fig. 4.

Figure 4: The filled-in AutoIMD window.

7. Now, click on Submit. This should create and launch a NAMD simulation on your machine. You should now see a second molecule called AutoIMD Simulation, which will be used to connect to the running simulation.

NOTE: If AutoIMD asks to create a directory called autoimd in your home directory, answer Yes.

NOTE: If you get an error message saying: Unable to open psf file imdnanotube.psf, you need to reload your PSF file on top of your current molecule one more time and click Submit again.

Windows users: AutoIMD will ask for the location of the namd2 executable. Simply point it to where you installed NAMD.

8. Finally, click on the Connect button to start displaying your simulation. After 100 steps of minimization, the water molecules in your VMD graphics window will begin to move. There will be a time counter in the AutoIMD window's status line indicating the minimization steps, and later, the simulation time (in ps).

NOTE: It might take a few seconds for the NAMD simulation to get started. During this time, VMD will not be able to connect and you will see some error messages of the type: Error connecting to localhost on port 2314. This is perfectly normal, and these errors can be ignored. VMD will connect as soon as NAMD is ready.

9. The nanotube will appear by default as bunch of chubby spheres. To see the water through it, select the ``imdhetero" representation in the AutoIMD molecule, and change the drawing method from VdW to Bonds.

10. When you are done (after, say, 10 ps or more), click on the Discard button. This will halt the simulation and bring you back to the molecule as it was before you started AutoIMD. If you had clicked on Finish instead, the final coordinates of the simulation would have been saved into your initial molecule (overwriting the old coordinates).

11. If you want to run a new simulation with different initial coordinates or modified parameters (or simply to re-run your old simulation) you would now only need to repeat steps 8 to 10 (i.e., click on Submit, Connect and Discard).