[gmx-users] Can I use RMSD increase to indicate the unfolding while the Rg remains unchanged?

[Justin Lemkul]

On 3/1/19 7:35 AM, ZHANG Cheng wrote:
> I think it is a common practice to use RMSD increase to indicate the structure deformation. And in many cases, this deformation is referred as unfolding.
>
>
> But I think the RMSD increase could also come from collapse (i.e. shrinkage). So would radius of gyration (Rg) be a better descriptor for unfolding? Would unfolding always result in Rg increase?
>

RMSD is a degenerate metric - one value can have many interpretations. 
This is why, as a standalone metric, it is often useless.

> I often see Rg unchanged or even decreases when RMSD increases.

This is a better (but also potentially incomplete) descriptor of what is 
going on. One can have an equivalent level of deviation if you take a 
given conformation and extend it or compress it. Rg tells you which 
direction it's going, but it also doesn't tell you how or why the 
structure is changing. RMSD tells you neither.

-Justin

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Justin A. Lemkul, Ph.D.
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