Restrained and unrestrained molecular dynamics simulations in the NVT ensemble of alamethicin.

Molecular dynamics simulations on the transmembrane antibiotic peptide alamethicin have been performed in the NVT ensemble (i.e., the number of particles N, the volume V, and the temperature T of the system are kept constant). Results on the structure and conformational flexibility of this molecule are discussed and compared with previous experimental CD, x-ray, nmr data and theoretical computations on fragments analogues. An extensive study of structural and dynamic properties from H-bonding pattern analysis is presented. Evidences for a largely alpha-helix structure with some extent of freedom in the C-terminal region are found. Further, a partition of the molecule into three regions on the base of structural features and dynamic behavior has been proposed, and the correlation among the motions of the three regions is described.