Peptoid Simulations

As the development on the topic of molecular structure developed, so too have the simulation techniques developed. A method known as coarse-grained molecular dynamics (CG-MD) helps simulating complex molecules, this method works by turning parts of the molecule that is being simulated into ‘beads’. Programs using the method of CG-MD have come about allowing for people to make things as complex as they want. One such program is Martini, a program where you can set parameters, and through these parameters make a reproducible simulation. Martini makes what is known as a forcefield, and with the need of a Martini forcefield model capable of handling peptoids. Through colaboration between parts of the Strathclyde Pure and Applied Chemistry department, including our very own Lau group, a model dubbed ‘Martinoid’ was developed.

figure 1. example of different peptoids being broken down into beads