Monte Carlo techniques structural optimization

When MD techniques are applied to simulate the structure of amorphous materials, a common starting point is to quench from the liquid state. However, due to the fact that an MD time step is in the order of femtoseconds and limitations on the total possible MD simulation time from computational resources, the quench rates used in MD are several orders of magnitude faster than those found experimentally, and this can lead to the generation of structures that are not found experimentally. In these cases Monte Carlo techniques can be beneficial in developing an initial structure of the amorphous material, which can be further refined using MD or geometry optimization methods. 

The feedback-optimized parallel tempering technique [26] outlined in the previous section has recently been applied to study the folding of the 36-residue chicken villin headpiece sub-domain HP-36 [27]. Since HP-36 is one of the smallest proteins with well-defined secondary and tertiary structure [28] and at the same time with 596 atoms still accessible to numerical simulations, it has recently attracted considerable interest as an example to test novel numerical techniques, including molecular dynamics [29,30] and Monte Carlo [31,32] methods. The experimentally determined structure [28] which is deposited in the Protein Data Bank (PDB code Ivii) is illustrated in the left panel of Fig. 6. 

---