Molecular Dynamics of Polyatomic Systems

摘要: This paper is concerned with the application of Molecular Dynamics (MD) computer simulations to polyatomic molecules characterized by a mixing “soft” (thermally activated) and “hard” inactivated) intramolecular modes. Statistical mechanics these complex mechanical bodies will be reviewed in some detail, both for models treating hard degrees stiff springs those which freeze them from outset geometrical constraints. Often, within class investigated here, one or few ‘soft’ coordinates control large conformational changes, implying passage over potential barrier kT: MD approach, an accurate estimation internal distribution such “reaction coordinate” requires special techniques force system sample saddle point regions. In context systems without constraints, advantages technique working cartesian other discussed.