APBS Tutorial
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Visualization

Important

The following requires the VMD functions provided in the my_functions Tcl script. Please download this before proceeding.

Electrostatic potential

The electrostatic potential can be visualized via VMD by running the pot.vmd script in VMD: 


          $ vmd -e pot.vmd
The result should be the rather uninteresting potential isosurface:

Figure 2. DNA electrostatic potential

which can be adjusted via the Graphics->Representations menu item.

Charge density

The charge density for the DNA is much more interesting than the electrostatic potential. The first step in our analysis will be to plot the average radial density around the DNA using the Python script density. This script can then be used to process the volume-based density file qdens.dx produced by our earlier APBS run: 


          $ python density qdens.dx | tee qdens.dat
The result of this command will be 3 columns of data (on the screen and written to qdens.dat): the radius (in A), the charge density at the given radius averaged over all angles and displacements along the center of the cylinder (+/- 10 A) (in ec A-3), and the cumulative charge density per unit distance along the DNA molecule (in ec A-2). This averaging is performed over the center of the DNA cylinder to avoid well-known "end effects".

The overall charge density profile can be visualized by starting Gnuplot: 


          $ gnuplot
and typing the following commands within Gnuplot: 

          gnuplot> set xlabel "Radius (A)"
          gnuplot> set ylabel "Charge density (e/A^3)"
          gnuplot> plot 'qdens.dat' using 1:2 title 'Charge density' with linespoints
The resulting plot shows the distribution of ions around the DNA molecule. The cumulative charge density can also be plotted by: 

          gnuplot> set ylabel "Cumulative charge density per length (e/A^2)"
          gnuplot> plot 'qdens.dat' using 1:3 title 'Charge density' with linespoints
When you are done with Gnuplot, simply exit by typing quit at the prompt. The results of these calculations are very sensitive to grid spacing and boundary conditions; this is mainly why the PB solution appears to be over-screening the DNA molecule.

The charge distribution can also be visualized with VMD by downloading qdens.vmd and running: 


          $ vmd -e qdens.vmd

You can translate the DNA molecule towards you by clicking in the VMD OpenGL window and typing 't' and holding down the middle mouse button while dragging. By doing this, you can cut through the charge density isosurfaces and get a better look at how the salt is arranged around the DNA. Additionally, you can modify the isocontour values (Graphics->Representations menu item) to examine regions of different salt concetration. The result of all this manipulation should look something like the following image:

Figure 3. NaCl charge density around DNA

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