[gmx-users] Why gyration radius keep dropping?

[Justin Lemkul]

On 1/19/18 1:22 PM, ZHANG Cheng wrote:
> Dear Gromacs,
> I am running MD at 500 K for my protein.
>
>
> I used this to analyse the gyration radius
> echo 1 | gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg
>
>
> I thought the radius should keep increase, as the protein unfolds at high temperature. However, all my repeats showed a dropping in the gyration radius, from ~2.6 nm to ~2.2 nm in 50 ns.
>
>
> Can I ask if this phenomenon is common?

Proteins don't necessarily just elongate when heated. Secondary 
structure destabilizes and you are probably adopting some kind of 
non-native, molten globule. Watch the trajectory.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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