Ilya Balabin, Marcos Sotomayor

Why adding ions? Some proteins may be (and sometimes are) sensitive to the ionic strength of the surrounding solvent. Even when that is not the case, adding ions is commonly used to make the net electric charge of the system zero. In molecular dynamics (MD) simulations with periodic boundary conditions, the energy of the electrostatic interactions is often computed using the particle-mesh Ewald (PME) summation, which requires the system to be electrically neutral. The vmd autoionize plugin provides a quick and easy means to make the net charge of the system zero by adding sodium and chlorine ions to the solvent. Ion placement is random, but but there are minimum distances between ions and molecule as well as between any two ions.

Graphical Interface The graphical interface provides some reasonable default values for adding ions to a solvated system, with the same functionality provided by the text command interface described below.

Text command usage. The text command syntax is simple. To load the plugin, run the following command:

package require autoionize

Running autoionize with no arguments gives a short overview of the syntax.  You can add ions in either of the following two ways:

autoionize -psf file.psf -pdb file.pdb -is 0.05

tells autoionize to compute the sodium and chlorine ion numbers so that the net chatge of the system is zero, and the average ionic concentration of the solution is (in this case) 0.05. Note: Autoionize defines this as the TOTAL ion concentration, for example, (#Na + #Cl)/V. Thus, this figure will be twice the ionic strength of the same solution (for monovalent ions). Alternatively,

autoionize -psf file.psf -pdb file.pdb -nna NNa -cl NCl

explicitly makes autoionize place the given numbers of the sodium (NNa) and chlorine (NCl) ions. In this case, the system may not be electrically neutral.

Additional options for autoionize include the following:

Adding ions to a 100,000-atom system takes about 30 seconds on a 766MHz laptop.


Changing ion type. For some biological molecules, one may want to place potassium ions instead of sodium. That can be easily done by using the sod2pot.tcl script.

source sod2pot.tcl

takes the coordinate file ("ionized.pdb") and the structure file ("ionized.psf") of the original system and creates files "sod2pot.psf/pdb", where sodium ions are replaced with potassium. With minor changes (knowledge of Tcl programming is not necessary), this script can be used for replacing any kind of ions with any other kind.

Caveats and Limitations. Autoionize places ions randomly, which is acceptable if the electric charge of the molecule is relatively small. If the charge is big, the ions no longer are nearly uniformly distributed in the solvent; instead, they form a screening clowd around the molecule. An example of such systems is a double-helix DNA, which carries a 1e charge per base pair. In such cases, one needs to place ions with regard to the electrostatic potential of the molecule.