Linear chains, conformational search

A variety of theories for flexible macromolecules (rod, spheres, cylinders, etc.) have been proposed, many of them being geared toward the study of polymers and DNA (see Conformational Sampling Conformational Search Linear Chains Conformational Search Proteins and Polymers Structural Representation), A brief discussion of representative methodologies for polymers, proteins, and nucleic acids follows. 

Conformational Sampling Conformational Search Linear Chains Conformational Search Proteins Systematic and Random Search Methods for Finding Conformers of Molecules. 

Many of the techniques described previously for structure prediction of macromolecules and docking predictions can be applied to the conformation analysis of small molecules with a view to energy minimization or constraint satisfaction. (See Conformational Analysis 1 Conformational Analysis 2 Conformational Analysis 3 Conformational Search Linear Chains Conformational Search Medium-sized Molecules and Conformational Search Proteins.)... 

In contrast, a system in contact with a thermal bath (constant-temperature, constant-volume ensemble) can be in a state of all energies, from zero to arbitrary large energies however, the state probability is different. The distribution of the probabilities is obtained under the assumption that the system plus the bath constimte a closed system. The imposed temperature varies linearly from start-temp to end-temp. The main techniques used to keep the system at a given temperature are velocity rescaling. Nose, and Nos Hoover-based thermostats. In general, the Nose-Hoover-based thermostat is known to perform better than other temperature control schemes and produces accurate canonical distributions. The Nose-Hoover chain thermostat has been found to perform better than the single thermostat, since the former provides a more flexible and broader frequency domain for the thermostat [29]. The canonical ensemble is the appropriate choice when conformational searches of molecules are carried out in vacuum without periodic boundary conditions. 

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