The emergence of powerful computers, like the ones you will use at the Ohio Supercomputer Center, has revolutionized the study of liquids, solids, and amorphous substances (glasses), a group of materials known as condensed phases.  Using a supercomputer, it is possible to follow the motion of tens, or even hundreds of thousands of molecules for times long enough to predict many useful physical properties.  Calculations of this type are known as molecular dynamics.

In this project you will use the Gromacs suite of molecular dynamics programs to model electroosmotic flow in a channel with charged walls.  There will be positive sodium and negative chloride ions in the water.  If the wall is charged, there will be an excess of either sodium or chloride to compensate the wall charge,

(total charge of fluid) = NNa+ - NCl- = -(total wall charge)

so the charge of the entire system is zero.  Let’s say the total wall charge was -20 in units of the proton charge.  Then we will need 20 Na+ ions to neutralize the wall charge.  We can also model the salt concentration by adding additional Na+/Cl- pairs.  A simulation with 20 sodium and no chloride ions means no added salt, while 30 sodium and 10 chloride means additional salt is present.  An applied electric field parallel to the walls, Ex is the figure, will induce electroosmotic flow.

Fluid in a channel with charged walls.  To keep things simple, the water molecules are not shown.  There are extra positive ions to exactly balance the wall charge.


The purpose of the project is to discover which conditions optimize electrosmotic flow.  You will see that the salt concentration, wall charge, and surface properties like roughness all have a profound effect on electroosmotic flow.  Students involve in this project will also visit Nanotech West, a facility where nanoscale devices are fabricated.


1. Electroosmotic flow in a model electrolyte (MolelElectrolyte.mpg).

The system shown here illustrates electroosmotic flow in a model fluid.  The fluid consists of cations (red), anions (blue), and solvent (either gray or white).  A slab of solvent at the beginning of the simulation is colored white so you can see how flow develops a time progresses.

2. Electroosmotic flow through a nozzle (nozzle-Div.mpg).

Electroosmotic flow through the nozzle system shown above is illustrated in the movie.  This system is far more realistic than the first example.  The orange material is a detailed model of amorphous SiO2, otherwise known as “glass”.  The fluid is composed of realistic water molecules.  There are so many water molecules in the figure, you cannot make out the individual hydrogen and oxygen atoms.  Sodium (deep blue) and chloride (blue-green) ions are visible in the fluid.  In the movie, only a subset of the water molecules are shown so you can trace how the water moves as time evolves.



Using UNIX at OSC:

Introductory UNIX:

Batch processing:


Gromacs manual:


VMD tutorials: