I would like to determine the structural changes of my protein at different temperature (eg. 350 K). In gromacs tutorial, the protein is equilibrated using nvt and npt under normal condition (300 K) prior mdp run. So in my case, should I equilibrate the protein at 350 K or 300 K?
Hai,
If your objective is to find the structural changes of your protein in response to different temperature, you can change the temperature at different values (300,310,320...350K) in several replicas. Therefore, you could observe the changes in structural stability at 300 to 350K, and report the specific temperature which has a stable RMSD.
Good Luck.
As you would like to determine the structural changes of the protein at high. temperature (eg. 350 K). So you should equilibrate the protein at 350 K to get appropriate solvation at the given temperature. If you also wants higher temperature like 400 K , 450 K. Do it stepwise increase (+30 K) the temperature and equilibrate .
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