[gmx-users] Why gyration radius keep dropping?

ZHANG Cheng 272699575 at qq.com
Fri Jan 19 19:22:53 CET 2018

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?


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