Macromolecular Entropy Can Be Accurately Computed from Force

作者：Hensen Ulf; Graeter Frauke; Henchman Richard H^*

来源：Journal of Chemical Theory and Computation, 2014, 10(11): 4777-4781.

DOI：10.1021/ct500684w

A method is presented to evaluate a molecules entropy from the atomic forces calculated in a molecular dynamics simulation. Specifically, diagonalization of the mass-weighted force covariance matrix produces eigenvalues which in the harmonic approximation can be related to vibrational frequencies. The harmonic oscillator entropies of each vibrational mode may be summed to give the total entropy. The results for a series of hydrocarbons, dialanine and a beta hairpin are found to agree much better with values derived from thermodynamic integration than results calculated using quasiharmonic analysis. Forces are found to follow a harmonic distribution more closely than coordinate displacements and better capture the underlying potential energy surface. The methods accuracy, simplicity, and computational similarity to quasiharmonic analysis, requiring as input force trajectories instead of coordinate trajectories, makes it readily applicable to a wide range of problems.

• 出版日期2014-11