Molecular Dynamics 10/1/22

Science with Richard Bleil

Today, my social media page brought up a memory that was a simulation of the behavior of water.  The package uses what’s called “molecular dynamics”, but this particular one also includes quantum mechanical calculations, density functional theory (an alternative to quantum theory), Monte Carlo (an alternative to molecular dynamics) and several semi-empirical packages (a faster form of calculations).  These were all put together in one package by a university researcher that was made available cheaply to research labs and for a little more money to industrial. 

Several similar packages were created, often by other research groups, and even one by the American Chemical Society.  Often, they were (and probably still are) used in pharmaceutical companies.  If we can understand, for example, how a specific drug works, then it can be modified to be more effective.  For example, I used the packages to understand how Distamycin, an anti-tumor drug, “identified” its “target” binding site.  With this knowledge, had I been hired by a pharmaceutical company, I could have modified it to bind to different sites, or allow it to bind with greater or weakened force. 

Ironically, I was watching a movie called “Enemy Mine” some years ago where a war rages between humans and an alien space race resisting human expansion in space.  During a dogfight, before the alien was shown to the audience, there was a flash to the alien fighter dashboard which featured a screen (not unlike the one in my car today) with an alien-looking object on the screen that rotated and changed.  The image they used was from a molecular dynamics package, probably the one that I have today, which, honestly, I found very impressive.  After all, if they’re advanced enough to do molecular dynamics in the middle of a deadly dogfight, that is advanced!

To put together the mathematical simulation of a package like this, one has to consider both kinetic and potential energy.  Kinetic energy is related to the speed with which molecules are moving.  The higher the temperature, the faster the average particle moves.  These velocities are scaled to the temperature desired by the user, but the motion includes both translational (where an entire molecules moves in space) and vibrational (where individual atoms within the molecule move relative to the other atoms).

The potential energy includes bonding energy where one atom is bound to another and intermolecular forces where one molecule is attracted to another.  These forces can pull atoms and molecules closer together or push them apart depending on how close they are.  The bonds are often treated as if they are on springs, oscillating back and forth depending on the strength of the spring.  If they are too far, the spring pulls them together, and in so doing creates a momentum of the atoms.  This momentum will push the atoms past their ideal resting point until the atoms are too close together.  At this point, the spring will push them back apart, again creating momentum that pushes the atoms too far apart beyond the ideal point.  This constant back and forth is the vibration of the bond. 

The time slices are incredibly small (on the order of picoseconds, or thousandths of a nanosecond).  At each time slice, a calculation is done to determine the exact velocity (speed and direction) of every single atom from the previous time slice, and the total potential energy, that is, every force of every bond and every molecular attraction in the entire system, and whether those forces are pushing or pulling the atoms.  The velocities from the previous time slice are then modified by the potential energies to create entirely new velocities for the new time slice.  Then the atoms are all “moved”, their positions changed based on the length of time of the time slice, and the velocities of the atoms.

Once the new positions of the atoms are determined, the atoms are all moved based on their new velocities within that time slice, when the process begins again.  As you might imagine, this kind of calculation is intensive and uses a lot of computer resources (computation speed, memory and even disc space).  The calculations are actually on very small systems compared to reality with only maybe a few hundred or thousand atoms.  This is probably why the technique lost its luster.  As fast and powerful as computers are becoming, they’re still woefully inadequate for simulations anywhere close to a realistic system.  Today these packages are very difficult to fine (I was lucky enough to find one of the premiere packages while it is still available), and the technique is not frequently taught.  It’s still a very cool package and I’m happy I have it, and understand how it works. 


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