Russian version English version
Volume 5   Issue 2   Year 2010
An Averaged Over Molecular Trajectories Method of Integral Equations of the Theory of Liquids in RISM Approximation

Tikhonov D.A., Sobolev E.V.

Institute of Mathematical Problems of Biology, RAS, Russia, 142290, Moscow region, Pushchino

Abstract. A new approach for studying the influence of solvent on molecular systems is suggested. It is based on the method of integral equations in the theory of liquids in RISM approximation. We obtained a new integral equation in which the matrix of intramolecular correlations is averaged over molecular trajectories calculated by molecular dynamics method. This approach enables one to take into account the mobility of dissolved molecules in assessing the solvation effect. Using the oxytocin peptide as an example we compare the results obtained in the framework of the new method with standard calculations of thermodynamical values averaged over trajectory. It is shown that in averaging over trajectory, all the structural and thermodynamic parameters of the peptide solvation obtained by the new method lie on the interval of statistical error.

Key words: hydration of macromolecules, steady dynamic trajectory, thermodynamic, integral equations of theory of liquids, RISM.

Table of Contents Original Article
Math. Biol. Bioinf.
doi: 10.17537/2010.5.188
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)


  Copyright IMPB RAS © 2005-2024