UTF-8SAM E1 Model 1255255192Under the Hood
How does the Molecular Workbench work?
The Molecular Workbench (MW) uses basic physics and a fantastic amount of computation. A few years ago, a supercomputer would have strained to do this much computing. Because MW can make mistakes, it is important that you know something about how it works.
The model uses Newton's Second Law to compute how atoms move. Here is how it works: [Illustrate with a circle like the Kreb cycle?]
It calculates the forces on each atom using the Lennard-Jones potential.
Then it uses F=ma to determine the acceleration.
The acceleration is used to compute how much the velocity changes.
This gives the velocity of each atom, which is used to move the atom forward a tiny time step.
The PE and KE is computed for every atom.
This whole process is repeated tens of thousands of times each second.
The accuracy of the computation depends on the forces not changing too much during each time step. If the time steps and velocities are small, the computations are quite accurate.
MW uses time steps measured in femtoseconds. This is one-millionth of one-billionth of a second or 10^-15 seconds.
That is a very small step. A femtosecond is to a second as one second is to about 32 million years.
Fortunately, computers are able to compute 100,000 steps easily and that is enough time for some interesting things to happen.
MW computes the total kinetic energy by adding up the KE of each atom, KE=(1/2)mv^2. The total potential energy comes from adding up the values of the Lennard-Jones potential for every pair of atoms. Then the total energy is computed by adding KE and PE.
It is amazing that the total calculated energy is constant, given how many calculations go into it.
Of course, we know from physics that the total energy MUST be constant, so this is not too surprising.
The fact that MW computes that energy is conserved means that the calculations must be fairly accurate.
What are limits of the Molecular Workbench?
In the model below, you can push the limits of the MW.
If you go too far, you will know, because the model will not compute the right energy. It will report that energy is not conserved.
Since we know that energy is conserved, we cannot trust a model that says that it isn't.
The model has 500 atoms. You can adjust the time step and kinetic energy. Can you break the model?
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116true1440.014truetrue40.040.040.040.060.0org.concord.modeler.text.BulletIcon$SquareBulletIcontrue60.0org.concord.modeler.text.BulletIcon$SquareBulletIcon60.0org.concord.modeler.text.BulletIcon$SquareBulletIcon60.0org.concord.modeler.text.BulletIcon$SquareBulletIcon60.0org.concord.modeler.text.BulletIcon$SquareBulletIcon40.040.040.040.040.040.040.040.040.040.040.040.040.040.0true40.040.040.0true40.0true40.040.040.040.0org.concord.mw2d.activity.AtomContainerpage10$0.mmlfalseorg.concord.modeler.PageXYGraph0Time (fs)Kinetic Energy/ParticlePotential Energy/ParticleTotal Energy/Particlefalse0.060000.0false-0.10.25400350Time (fs)Energy (eV)true320450-333301-1falseRaised Bevelorg.concord.modeler.PageSliderorg.concord.mw2d.models.MolecularModel01.48199999943375580.100000001490116124.050Time step (femtosec)30060falsetrue{value="3.4319999986886978", label="3.5"}{value="1.4819999994337558", label="1.5"}{value="2.9639999988675116", label="3"}{value="1.0139999996125697", label="1"}{value="2.4959999990463255", label="2.5"}{value="0.5459999997913837", label=".5"}{value="3.9779999984800813", label="4"}{value="1.949999999254942", label="2"}{value="0.15599999994039535", label=".1"}Execute MW scriptorg.concord.modeler.PageSliderorg.concord.mw2d.models.MolecularModel02500.00.02500.050Kinetic Energy20060falsetrue{value="2500.0", label="High"}{value="0.0", label="None"}Temperature40.040.0org.concord.modeler.ImageQuestion350250Lowered Etched<html><font face="Verdana" size="2">Insert here a snapshot of a graph for a system with 500 atoms that is <b>not</b> accurate. In the caption, explain why this is inaccurate and how it should be fixed. </font></html>org.concord.modeler.PageTextField400150<html>
What do you think the largest time step should be? Justify your answer.
</html>1.5 fs seems safe—the total energy remains constant even for 500 atoms. 40.040.0org.concord.modeler.ActivityButtonHintHint about how to break the system.If the atoms are going further with each step, it is more likely that they will get into trouble. Hinttruepage9.cmltruetrueindex.cmltruetruepage11.cmltruetrue20.020.020.020.020.020.020.020.020.020.020.020.020.020.020.0