Conformational searching/quenched

Using conformational searching/quench dynamics and 7) relaxation measurements, each back-folded isomer was determined to be smaller than its extended counterpart. Thus, the effective distance of electron transfer was not reflected in the hydrodynamic radius of the molecule. Rather, the back-folded isomers were argued to be less mobile with the iron-sulfur core buried more deeply within them. The extended isomers were more mobile with the iron-sulfur core more able to come closer to the molecular surface. By this reasoning, the back-folded isomers had a larger effective electron transfer distance than the extended isomers. 

High temperature searches of conformational space (see Quenched Dynamics" on page 78), can produce unwanted conformational changes, such as cis-tmnx peptide flips, ring inversions, and other changes that you cannot reverse easily by geometry optimization. You can use restraints to prevent these changes. 

Quenched dynamics can trap structures in local minima. To prevent this problem, you can cool the system slowly to room temperature or some appropriate lower temperature. Then run room temperature molecular dynamics simulations to search for conformations that have lower energies, closer to the starting structure. Cooling a structure slowly is called simulated annealing. 

The temperature of a simulation depends on your objectives. You might use high temperatures to search for additional conformations of a molecule (see Quenched Dynamics on page 78). Room temperature simulations generally provide dynamic properties of molecules such as proteins, peptides, and small drug molecules. Low temperatures (<250 K) often promote a molecule to a lower energy conformation than you could obtain by geometry optimization alone. 

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