Past Meetup

DIY-Molecular Dynamics Simulation of Water

This Meetup is past

17 people went

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Details

The goal of this meeting is to break down the physics, mathematics and coding of a molecular dynamic simulation of two water molecules in a 4x4 Angstrom box for a femto-second (fs). It takes a computer a fraction of a second to do this, and we will do it in about an hour and thirty minutes.

You will be given a detailed list of steps with numerical results from generating random initial values to atoms to a single time step simulation of 1 fs. All you have to do is follow the steps and fill in a few blanks.

No previous advance math knowledge is required. This is an all inclusive class in which we will provide the step-by-step procedure that generates the water molecule trajectories. Math calculations such as quaternions, matrix multiplications and differential equations are already solved and given in detail.

You will be given access to the code that generates the water molecule trajectories, and you could 'change' the laws of physics in the virtual world of molecular dynamic simulations by changing the algorithms and mathematical formulas.

At the end of the class you will have A working model of Newtonian mechanics, Hamilton's quaternions, mathematical thermostats, force fields and integration algorithms, etc. You will be empowered to question the math and how it relates to the physical world. Hopefully, you will be encouraged to join our group and contribute to solving the mysteries of water's anomalies.