[gmx-users] adius of gyration - compactness

[Tsjerk Wassenaar]

Hi Shahab,

> I want to know exactly how do radius of gyration of protein from free state
> to complex state change .
> Rg increased od decreased?

That depends on the protein. Some will, e.g., close or fold upon
binding, while others may open up, or unfold.

> I want to know my data [ In my simulation systems, the average of radius of
> gyration in free protein
> is 2.31 and for protein in complex is 2.58.] is true?

It's true, because you found it. Whether it correctly reflects the
state of the system you're after depends on the quality of your model,
the time scale simulated and the tims scale of conformational changes
involved in (un)binding. There's no rule of thumb.

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands