An open question. I understand that temperature change is important for replicating an environment appropriate for the protein simulations from mescophilic, thermophilic and hyper-thermophilic hosts. Also, I am performing some simulated annealing on a predicted protein structure (from an I-TASSER, i.e., non-homology model) in order to better settle the protein's tertiary structure.
Besides these two very generic examples, when else would changing the simulation temperature during a protein simulation be useful? I appreciate hearing the opinions of others.
Many thanks.
For stable or good protein's tertiary structure, annealing is the only method? I guess, general protein has some temperature range for survival. what's proper annealing temperature range for protein? I think possible annealing temperature would be important for analyzing simulation data or determining usefulness.
Applying different positional restraints, rather than simulating at different temperatures, might be an efficient way to probe the temperature dependence of catalytic rates . . .
Article Enzyme surface rigidity tunes the temperature dependence of ...
Hi Martin,
That was an extremely interesting paper to read. Thanks for that recommendation, it contained a number of techniques I am currently using/exploring.
Increasing the temperature means the kinetic energy of the system will increase, potentially allowing it to go from one potential energy well to another. Therefore, it is a reasonable straightforward - yet somehow heuristic - way of sampling more potential energy surface.
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