Step Nine: Analysis
The radius of gyration of a protein is a measure of its compactness. If a protein is stably folded, it will likely maintain a relatively steady value of Rg. If a protein unfolds, its Rg will change over time. Let's analyze the radius of gyration for lysozyme in our simulation:
gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg
Choose group 1 (Protein) for analysis.
We can see from the reasonably invariant Rg values that the protein remains very stable, in its compact (folded) form over the course of 1 ns at 300 K. This result is not unexpected, but illustrates an advanced capacity of GROMACS analysis that comes built-in.
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