On the calculation of entropy from covariance matrices of the atomic fluctuations

An ad hoc method for calculating the entropy of a biomolecular system from the covariance matrix of the atomic fluctuations is analyzed. It is shown that its essential assumption can be eliminated by a quasiharmonic analysis. The computer time required for use of the latter is of the same order as that of the former.

[1]  P. Kollman,et al.  Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. , 2000, Journal of medicinal chemistry.

[2]  H. Berendsen,et al.  Free energy determination of polypeptide conformations generated by molecular dynamics , 1984 .

[3]  H. Berendsen,et al.  ENTROPY ESTIMATION FROM SIMULATIONS OF NON-DIFFUSIVE SYSTEMS , 1984 .

[4]  M. Karplus,et al.  Simulation analysis of triose phosphate isomerase: conformational transition and catalysis. , 1992, Faraday discussions.

[5]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[6]  Dusanka Janezic,et al.  Harmonic analysis of large systems. I. Methodology , 1995, J. Comput. Chem..

[7]  R. Stevens,et al.  A molecular mechanism for pyrimidine and purine nucleotide control of aspartate transcarbamoylase. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[8]  William H. Press,et al.  The Art of Scientific Computing Second Edition , 1998 .

[9]  Bradley E. Bernstein,et al.  Synergistic effects of substrate-induced conformational changes in phosphoglycerate kinase activation , 1997, Nature.

[10]  J. Chaires,et al.  Energetics of drug-DNA interactions. , 1997, Biopolymers.

[11]  J. Schlitter.  Estimation of absolute and relative entropies of macromolecules using the covariance matrix , 1993 .

[12]  M. Karplus,et al.  Method for estimating the configurational entropy of macromolecules , 1981 .

[13]  William H. Press,et al.  Numerical recipes in C. The art of scientific computing , 1987 .

[14]  M. Karplus,et al.  Evaluation of the configurational entropy for proteins: application to molecular dynamics simulations of an α-helix , 1984 .

[15]  An optimized harmonic reference system for the evaluation of discretized path integrals , 1984 .

[16]  M. Perutz.  Stereochemistry of Cooperative Effects in Haemoglobin: Haem–Haem Interaction and the Problem of Allostery , 1970, Nature.

[17]  A. Cooper,et al.  Thermodynamic analysis of biomolecular interactions. , 1999, Current opinion in chemical biology.

[18]  X. Daura,et al.  Entropy calculations on a reversibly folding peptide: Changes in solute free energy cannot explain folding behavior , 2001, Proteins.

[19]  Wilfred F. van Gunsteren,et al.  Absolute entropies from molecular dynamics simulation trajectories , 2000 .

[20]  P. Privalov,et al.  Energetics of protein structure. , 1995, Advances in protein chemistry.