Calculation of molecular complexation free energy by thermodynamic integration with harmonic restrictions on atomic coordinates

Authors

  • F.V. Grigoriev

Keywords:

free energy of complex formation
thermodynamic integration

Abstract

A new method for calculating the Gibbs free energy of intermolecular complex formation using the thermodynamic integration method with harmonic restrictions on atomic coordinates is proposed. The molecular dynamic trajectory for the thermodynamic integration is obtained using the MMFF94 force filed for calculating the energy of interaction between atoms. It is shown that the method provides the correct calculation of the free energy term from the harmonic restriction and minimizes the fluctuations during the integration procedure. The free energy for benzene-cyclodextrine host-guest complex formation is determined.

New computational technologies

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Published

2012-08-27

Issue

Vol. 13 (2012): Issue 3.

Section

Section 1. Numerical methods and applications

Author Biography

F.V. Grigoriev

Lomonosov Moscow State University,
Research Computing Center
• Researcher

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