Computational Methods for Configurational Entropy Using Internal and Cartesian Coordinates

• DOI: 10.1021/acs.jctc.6b00563
• Publication Date: 2016-11-22T00:46:39Z
• Authors: Simon Hikiri; Takashi Yoshidome; Mitsunori Ikeguchi
• Keywords: Kinetics; Protein Folding; 0303 health sciences; 03 medical and health sciences; Entropy; Quantum Theory; Molecular Dynamics Simulation; Oligopeptides; Protein Unfolding

The configurational entropy of solute molecules is a crucially important quantity to study various biophysical processes. Consequently, it necessary establish an efficient quantitative computational method calculate as accurately possible. In the present paper, we investigate performance quasi-harmonic and related methods, including widely used methods implemented in popular molecular dynamics (MD) software packages, compared with Clausius method, which capable computing change upon temperature change. Notably, focused on choice coordinate systems (i.e., internal or Cartesian coordinates). Boltzmann-quasi-harmonic (BQH) using coordinates outperformed all six examined here. introduction improper torsions BQH improves its performance, anharmonicity proper proteins identified be origin superior method. contrast, MD packages show rather poor performance. addition, enhanced sampling replica-exchange simulations was found for convergent behavior calculations. Also folding/unfolding transitions small protein, Chignolin, reasonably accurate. However, independent term without correlation most accurate folding among considered this study, because QH approximation no longer valid divergent unfolded structures.