[Molecular dynamics of oligopeptides. 1. The use of long trajectory and high temperature data for determination of statistical weight of conformational substates].

Abstract

The method of molecular dynamics investigations of the particularities of macromolecule physical-chemical properties is discussed. The results, obtained from the calculations of modified dipeptides in different regimes (different temperatures, length of trajectories and ways of thermostat simulation) are compared. The optimal conditions for this peptides calculations are determined: collisional dynamics regime, trajectories not less than 5000 ps, temperature about 1000 K. In this case the figurative point is able to scan the molecule configuration space and the statistically reliable results could be obtained.