ISSN:
1089-7690
Source:
AIP Digital Archive
Topics:
Physics
,
Chemistry and Pharmacology
Notes:
The double scanning method (DSM) is a computer simulation technique suggested recently by Meirovitch [J. Chem. Phys. 89, 2514 (1988)]. This method is a variant of the usual or "single'' scanning method (SSM) of the same author, which was extended by us to polypeptides [Biopolymers 27, 1189 (1988); this paper is designated here as paper II]. The two methods are step-by-step construction procedures from which the entropy and the free energy can be estimated. The transition probabilities are obtained by scanning the so-called "future'' chains, which are continuations of the chain in future steps up to a maximum of b steps. With the SSM, the process is carried out by exact enumeration of the future chains; this is time consuming, and therefore b is limited to small values. With the DSM, on the other hand, only a relatively small sample of the future chains is generated by applying an additional scanning procedure. This enables one to increase b at the expense of approximating the transition probabilities. Increasing of b, however, is important in order to treat medium- and long-range interactions more properly. In this paper (as in our paper II), we apply the DSM to a model of decaglycine without solvent, described by the potential energy function ECEPP at 100 and 300 K. Using the SSM with the maximal value, b=4, we found in paper II that, at 100 K, the α helix rather than the statistical coil is the most stable state. The present DSM simulation at T=100 K (based on b=5) is more efficient than the SSM, and a structure with significantly lower energy than that of the α helix is found. It is argued that b can be increased further to 7 at this temperature. At 300 K the DSM, like the SSM, shows that the statistical coil is the most stable state of decaglycine. However, the DSM is found to be less efficient than the SSM. It is argued, however, that the DSM is expected to be advantageous (even at 300 K) to simulate more complex polypeptides that are stable in small regions of phase space (such as the α-helical state). Finally, it should be pointed out that the present method can be employed to treat a wide range of macromolecular models, such as those for synthetic polymers and nucleic acids.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1063/1.458134
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