Multibody local approximation: application to conformational entropy calculations on biomolecules.

Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA. esuarez@pitt.edu

The Journal of chemical physics 2012 Aug 28

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Multibody type expansions like mutual information expansions are widely used for computing or analyzing properties of large composite systems. The power of such expansions stems from their generality. Their weaknesses, however, are the large computational cost of including high order terms due to the combinatorial explosion and the fact that truncation errors do not decrease strictly with the expansion order. Herein, we take advantage of the redundancy of multibody expansions in order to derive an efficient reformulation that captures implicitly all-order correlation effects within a given cutoff, avoiding the combinatory explosion. This approach, which is cutoff dependent rather than order dependent, keeps the generality of the original expansions and simultaneously mitigates their limitations provided that a reasonable cutoff can be used. An application of particular interest can be the computation of the conformational entropy of flexible peptide molecules from molecular dynamics trajectories. By combining the multibody local estimations of conformational entropy with average values of the rigid-rotor and harmonic-oscillator entropic contributions, we obtain by far a tighter upper bound of the absolute entropy than the one obtained by the broadly used quasi-harmonic method.

Citation

Ernesto Suárez, Dimas Suárez. Multibody local approximation: application to conformational entropy calculations on biomolecules. The Journal of chemical physics. 2012 Aug 28;137(8):084115