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Molecular Dynamics Simulation


This pages is made from part of my lecture note

This simulator was made with HTML5+CSS+JavaScript. So you need Web Browser that can run HTML5. For PC/Mac Chrome, Safari or FireFox4.0 is recommended. iPad with Mobile Safari is also one choice. IE9 may not work because HTML5 implementation is very poor. IE below 9 are not supported HTML5.

This MD proram is not for MD scientist. I made this program for Chemical Engineering Course Students who take my lecture at Yokohama Natonal University Japan.

At first, put molecule and elevate temperature.

If you push start button, you will see 600 molecules in the box. (The slider is not implement in FireFox4.0 nor iPad mobile safari. you will see the textbox so enter value and hit return key.) At 10℃ this molecule is liquids and fall down to bottom of the box.

If you drag the Box, you can chnage the view point. Even it is liquid, each molecule is moving. Sometime, molecule jump up. Please elevate temperature slowly. (if you elevate very quick, Nuclear Fusion happen!)

Some of the molecules hit the wall, we can observe it as pressure. Sometime molecules bump each other then increase/decrese speed. That lead thermal conductivity.

If you see this box from top view, you will find out the liquid are coming togeter. This aggregation force is observed as Surface tension.

The temperature become much higher, the liquid spread all the floor, and average distance of liquid molecule become longer. you will observe this phenomena as temperature dependency of density.

Where is boiling point? With this simulator, even in vapor phase, there are many molecule that aggregate. maybe some of the parameters are bad. These aggregation lead to viscosity of liquid/vapor.

And at critical point, all the molecule will spread evenly. Maybe around 450℃.

Actually, I already build properties estimation schemes for these properties, so I need not get these values from MD. This program is just sight effect viewer.


This simulation is for distillation.

Red sphere means 3 times heavier molecules (10%).

Please keep temperature and wait red spheres go into liquid. Then elevate temperature. Only blue molecules are evaporate and go into vapor phase. If you put cold part in the box, molecular velosity will go down and become liquid and you can separate molecule. That is simple distillation.

Please get the highest temperature that still no red sphere in vapor phase.

Please wait several min. after you change temperature.


In Japan, we have nuclear plant plant damage by huge earth quake and Tsunami. And need purify water from radio active. They use Zeolite to absorb Ce.


For this case, we need to introduce charge term. program calculate QEQ charge every iteration so it is very slow. you can not use iPad for this calculation. At first, set temperature 1000℃ and click start button. Each atoms move intensely.

Reduce temperature around 700℃, you will see several core that made of Al with Oxygen.

And around 550℃, you will see the cluster growing.

Around 400℃, the cluster become clear. Sometime cluster fuse, sometime cluster breakup. That depend on how many oxygen exist in cluster. It seems that to keep around this temperature is important.

Reduce to 300℃, the cluster become very stable.

Around 100℃、regularity appear.

I clalculate iMac 27inch 3.06GHz Core 2 Duo and take 15 min. to get this result. If you change temperature profile or composition, cluster will change. Please try and search effective Ce trapper.


From the point of Japanese condition of power supply, we need to develop high efficency battery.


Li is very light and move intensely so keep the lower temperature compare to Zeolite. At first, Fe(Black)-P(Green)-O(red) cluster appear, then reduce temperature Li(orange) attached to cluster. I think P is not introduce evenly. That is the point to make this catalyst. Please try this MD software.

This program is non restrict version. At the first day of my class, I give you the pass code to run this program. You can use 500 atoms from H(1) to Lr(103). If you pass QEQ calculation, you can use 1000 atoms.