Molecules in Motion

Brought to you by Andrea Delapaz

Whoo hoo Molecular Dynamics! The following are some movies generated to show the quenching of many systems at various densities. With the guidence of Professor Lev Gelb, I was able to make these over the course of the semester. So click on one and watch them move.....

Introduction: This study was an investigation of the Lennard- Jones fluid; more specifically the liquid-vapor separation process. The computer animations generated below show what happens to a system of a certain density and system size when the temperature is decreased dramatically from T=2.0 to T=0.7. The molecules are colorized according to their potential energy, with red meaning a low potential energy, blue meaning high potential energy, and green somewhere in between.

The Phase Diagram below shows that when a fluid is quenched (taken from a high value of T to a low value of T) it separates from a vapor stage into a stage where both vapor and liquid are present. The density of the system determines the amount of vapor and liquid present after the quench. At lower densities mostly vapor is present and some liquid droplets form, while at higher densites a larger amount of liquid is present while some vapor still remains as bubbles.

(One last note - the colors in the pictures below represent the potential energy of each particle. Red particles have high potential energy, and blue particles have low potential energy. Lots of low potential energy is what stabilizes a liquid or solid, while lots of entropy, or randomness, is what stabilizes a gas. -- LG)

Quench at density = 0.1

Quench at density = 0.2

Quench at density = 0.3

Quench at density = 0.35

Quench at density = 0.4

Quench at density = 0.5

Quench at density = 0.6

Quench at density = 0.7

Now let's get technical: So how did these movies come about? Well, the computer animations were a product of a series of computer simulations and system investigations of various densities ranging from 0.1 to 0.7. To begin the process an initial configuration for each density was created, containing information such the volume of the system, a 30 x 30 x 30 cell, and the number of particles for the system depending on the density. This initial configuration file was then used in the molecular dynamics program 'md.x' where the system was equilibrated at 15,000 steps. Md.x creates a series of output files; two in particular were looked at in this investigation, an energy file and a configuration file. The energy file was read with a graphing program and checked after each run to make sure the system was equilibrated. For a more visual look at the equilibrated system, the configuration file was converted to an image using the 'toxyz' command, which was then read using the RasMol program which displayed the system as a graphic.

Once all the densities were equilibrated they were then quenched. Quenching meant taking a certain density system at a high temperature and re-equilibrating that system at a lower temperature. This process made the system phase separate between droplets of liquid and vapor molecules. After all densities were quenched they were ready to be made into movies. A program called 'topov' generated files that would then be used by the 'povscript' program to render frames that would make up the movie. Upon the completion of the frames other programs called 'Main Actor and Main Actor Sequencer' were used to place all the frames together and add the special effect and text. Then viola... you have movies!

But, we're not quite done yet... There are some things that need just a touch of further explaination, like the Lennard-Jones potential equation. This equation contains parameters sigma and episilon representing molecular diameter given as a unit of distance and energy given as units of energy, respectively. But there's a catch, this equation can be written as an one of reduced units.What the idea behind this is to use sigma as 1 unit of distance and episilon as one unit of energy, thereby resulting in an equation in terms of sigma and episilon. This makes the equation a dimensionless equation which is helpful in computer simulations and other investigations of this potential.