[gmx-users] Standard Procedures to perform MD under High Temperature 498 K, either NVT or NTP ?

[Chih-Ying Lin]

Hi
I read some papers and many simulations were performed under high
temperature to induce the unfolded protein.
However, the authors did not mention how they conducted the simulations
under high temperature, 498 K.
They did not mention which NVT or NPT were adopted for such high
temperature.
None of any parameters about the temperature coupling and pressure coupling
were described on the papers.


Are there any standard procedures to perform High temperature - MD
simulation?
Where can I find the standard procedures?


At 498K, protein is cooked.
Under NPT, the water evaporated. => so,  turn on pressure coupling with a
(very) high pressure to keep the water molecules.
Under NVT, the pressure increased dramatically.
So, to run MD simulations under the high temperature means to run the MD
simulation under high pressure at the same time?



But, I did read one paper that the authors performed the MD simulation under
high temperature and high pressures separately
and further discuss the effect the high temperature and the high pressures
on protein separately.



Thank you
Lin
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