Energy landscapes and global thermodynamics for alanine peptides.

摘要: We compare different approaches for computing the thermodynamics of biomolecular systems. Techniques based on parallel replicas evolving via molecular dynamics or Monte Carlo simulations produce overlapping histograms densities states. In contrast, energy landscape methods employ a superposition partition function constructed from local minima potential surface. The latter approach is particularly powerful systems exhibiting broken ergodicity, and it usually implemented using harmonic normal mode approximation, which has not been extensively tested biomolecules. present contribution compares these alternative small alanine peptides modelled CHARMM AMBER force fields. Densities states produced canonical sampling multiple temperature provide accurate reference data to evaluate effect approximation in calculations. This benchmarking lays foundations application larger It will also well characterised model developing enhanced methods, treatment anharmonicity corresponding individual minima.