Post-Analysis of MD Trajectories
After the MD simulations have been reasonably carried out, the next step is to analyze the trajectory of the system of interest. Here, using PEO-grafted gold nanopores as the example, the structural properties are analyzed for demonstration.
Basics to know
To better analyze the system, one has to:
- have a good understanding of the system (e.g., geometry file)
- validate the MD results reasonable or not
- select what types of properties to analyze
- interpret the results and explain what's the science behind the simulations
Here is an example of the PEO chains under different pore curvatures:
Figure 1: Conformation (a) and expansion ratio (b) of the PEO chains under different pore curvatures.
One can clearly see that due to nanoconfinement effect, PEO accommodates its conformation for the pore geometry constraint. The pore coverage with different pore sizes at two different grafting densities is as follows:
Figure 2: Brush height as a function of pore sizes. PEO backbone is colored in red (for oxygen atoms) and cyan (for carbon atoms). Water is shown in red (red atoms) and white (hydrogen atoms).
References
[1] G. Chen, and E. Dormidontova. PEO-grafted gold nanopore: grafting density, chain length and curvature effects. [URL]