6 research outputs found
Fast calculation of thermodynamic and structural parameters of solutions using the 3DRISM model and the multi-grid method
In the paper a new method to solve the tree-dimensional reference interaction
site model (3DRISM) integral equations is proposed. The algorithm uses the
multi-grid technique which allows to decrease the computational expanses.
3DRISM calculations for aqueous solutions of four compounds (argon, water,
methane, methanol) on the different grids are performed in order to determine a
dependence of the computational error on the parameters of the grid. It is
shown that calculations on the grid with the step 0.05\Angstr and buffer
8\Angstr give the error of solvation free energy calculations less than 0.3
kcal/mol which is comparable to the accuracy of the experimental measurements.
The performance of the algorithm is tested. It is shown that the proposed
algorithm is in average more than 12 times faster than the standard Picard
direct iteration method.Comment: the information in this preprint is not up to date. Since the first
publication of the preprint (9 Nov 2011) the algorithm was modified which
allowed to achieve better results. For the new algorithm see the JCTC paper:
DOI: 10.1021/ct200815v, http://pubs.acs.org/doi/abs/10.1021/ct200815
Fast Computation of Solvation Free Energies with Molecular Density Functional Theory: Thermodynamic-Ensemble Partial Molar Volume Corrections
Molecular Density Functional Theory (MDFT) offers an efficient implicit-
solvent method to estimate molecule solvation free-energies whereas conserving
a fully molecular representation of the solvent. Even within a second order ap-
proximation for the free-energy functional, the so-called homogeneous reference
uid approximation, we show that the hydration free-energies computed for a
dataset of 500 organic compounds are of similar quality as those obtained from
molecular dynamics free-energy perturbation simulations, with a computer cost
reduced by two to three orders of magnitude. This requires to introduce the
proper partial volume correction to transform the results from the grand
canoni- cal to the isobaric-isotherm ensemble that is pertinent to experiments.
We show that this correction can be extended to 3D-RISM calculations, giving a
sound theoretical justifcation to empirical partial molar volume corrections
that have been proposed recently.Comment: Version with correct equation numbers is here:
http://compchemmpi.wikispaces.com/file/view/sergiievskyi_et_al.pdf/513575848/sergiievskyi_et_al.pdf
Supporting information available online at:
http://compchemmpi.wikispaces.com/file/view/SuppInf_sergiievskyi_et_al_07-04-2014.pdf/513576008/SuppInf_sergiievskyi_et_al_07-04-2014.pd
Fast and general method to predict the physicochemical properties of druglike molecules using the integral equation theory of molecular liquids
We report a method to predict physico-chemical properties of druglike molecules using a classical statistical mechanics based solvent model combined with machine learning. The RISM-MOL-INF method introduced here provides an accurate technique to characterize solvation and desolvation processes based on solute-solvent correlation functions computed by the 1D Reference Interaction Site Model of the Integral Equation Theory of Molecular Liquids. These functions can be obtained in a matter of minutes for most small organic and druglike molecules using existing software (RISM-MOL) (Sergiievskyi, V. P.; Hackbusch, W.; Fedorov, M. V. J. Comput. Chem. 2011, 32, 1982-1992.). Predictions of caco-2 cell permeability and hydration free energy obtained using the RISM-MOL-INF method are shown to be more accurate than the state-of-the-art tools for benchmark datasets. Due to the importance of solvation and desolvation effects in biological systems, it is anticipated that the RISM-MOL-INF approach will find many applications in biophysical and biomedical property prediction
Multigrid solver for the reference interaction site model of molecular liquids theory
In this article, we propose a new multigrid-based algorithm for solving integral equations of the reference interactions site model (RISM). We also investigate the relationship between the parameters of the algorithm and the numerical accuracy of the hydration free energy calculations by RISM. For this purpose, we analyzed the performance of the method for several numerical tests with polar and nonpolar compounds. The results of this analysis provide some guidelines for choosing an optimal set of parameters to minimize computational expenses. We compared the performance of the proposed multigrid-based method with the one-grid Picard iteration and nested Picard iteration methods. We show that the proposed method is over 30 times faster than the one-grid iteration method, and in the high accuracy regime, it is almost seven times faster than the nested Picard iteration method