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.
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