Improving Force Parameters
Why water?
Water is the most abundant compound on the planet and is essential to many naturally occurring reactions. Therefore, it is of utmost importance to use a realistic water model when simulating molecular interactions on the computer. An unrealistic model of water can cause an entire system to behave completely differently than it does in the real world.
Our Goal
Much of our research focused on comparing the simulated behavior of water with the actual behavior observed in the real world. Specifically, we looked at the frequency of vibrations in the molecule. Water has a very dynamic and complex behavior, and there are many different vibrations that occur within each molecule. Our goal was t try and make these vibrations within the molecules more realistic.
Connecting Spectroscopy to MD
We studied the bond stretching and angle bending in water due to the ease of collecting data and modifying their frequencies. When studying this in real water, infrared spectroscopy can be used to find the exact frequencies of vibration. We found these frequencies on online databases and then compared them to data we collected from experiments run in NAMD. To collect our data, we wrote a TCL script that went through each frame of the simulation and recorded the distance of a particular O-H bond as well as the H-O-H angle in a certain molecule. We did a discrete Fourier transform on this data to obtain the frequency of vibration. After studying the data, we found that the bond stretching frequency matched well with the real world data. However, there was a significant discrepancy in the frequency of angle bending. You can see both of these observatios in the following graphs. We think that the realism of the model can potentially be improved by altering the constant in the angle potential equation so that it more accurately reflects the behavior of real water.
In this graph, the default value of Kb = 500 is pretty close to the actual peak.
However, in this graph, a value like kθ = 46 might be closer than the default value pulled from the parameter file.
You can view the ful presentation below:
Pair Correlation Functions
We recently gave the following presentation on PCFs, like the Leonard Jones potential, and how they are affacted by different conditions.