Here, we will learn how to modify the electric charge of
individual atoms, as they appear in the NAMD simulation.
Exercise: We have seen that water permeates through the nanotubes in a single file of oriented water molecules. We would like to modify the nanotube such that we get a bipolar configuration of water, such as the one seen in the glyceroaquaporin pore (i.e., the water oxygens at both ends of the pore point toward the center of the pore). One way to achieve this is to assign charges to a few carbon atoms in the nanotube. Think of a way that you can charge 3 or more of the nanotube's carbon atoms to achieve this. You will soon run a simulation using these charges to test your predictions.
The following instructions detail how to change the charge of
an atom in a PSF file (which in turn is used by NAMD simulations).
1. Make a copy of the imdnanotube.psf file (let's call it mynanotube.psf, for example) and open it in your favorite text editor (e.g., nedit). In the PSF file, you should see a bunch of lines that look like:
64 NT22 1 ARM C063 CA 0.000000 12.0110 0 65 NT22 1 ARM C064 CA 0.000000 12.0110 0 66 NT22 1 ARM C065 CA 0.000000 12.0110 0
2. You want to change the charges of a few carbons in the
nanotube, but first you need to identify these atoms by their unique
index. Using the Mouse Query mode in VMD and then clicking on atoms, get the indices of
the carbon atoms whose charges you have decided to change (with the query mouse mode, you can read the atom indices in the console window or the Graphics Labels window).
Note: VMD counts atoms starting from 0, while the PDB and PSF
files start at 1. Thus, you need to add 1 to the index you get from
VMD to get the atom index in the PSF file.
3. In the PSF file (in the text editor), find the row
corresponding to the atom index that you are looking for (the atomic
index is in the first column). Do not forget to add
1. Example: if you wish to change the charge of the atom with
index 65 in VMD, you need to edit the row starting with 66.
4. Now, change the column that says 0.000000 to a new
number. This number should be a multiple or fraction of the electron
charge e. Important: Make sure not to change the
column alignment, as every space in the PSF file is important! For
example, to assign a charge of -e/2 to the 65 (VMD's
index) atom, you would substitute the line
66 NT22 1 ARM C065 CA 0.000000 12.0110 0
66 NT22 1 ARM C065 CA -0.500000 12.0110 0
5. Save your changes to the new PSF file.
6. Back in VMD, load your new PSF file (mynanotubes.psf)
into your previous molecule (by selecting it and choosing the
File Load Data Into Molecule... menu
item, etc.). This will replace the charges that were
previously there. Select your nanotube (carbon)
representation in the Graphical Representations window and
click on the Apply button to redraw the nanotube with
the correct charge colors. You should now see different colors
for different charges, as in
7. You can repeat this process as many times as you want, until
you get the charge distribution that you like to experiment
with. Once you have a decorated nanotube, you are ready to run the
simulation on your local machine with AutoIMD. Just follow
instructions 8 to 10 from section 4.1
(i.e., click on Submit, Connect and