16 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
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
3DRISM Multigrid Algorithm for Fast Solvation Free Energy Calculations
In this paper we present a fast and accurate method for
modeling
solvation properties of organic molecules in water with a main focus
on predicting solvation (hydration) free energies of small organic
compounds. The method is based on a combination of (i) a molecular
theory, three-dimensional reference interaction sites model (3DRISM);
(ii) a fast multigrid algorithm for solving the high-dimensional 3DRISM
integral equations; and (iii) a recently introduced universal correction
(UC) for the 3DRISM solvation free energies by properly scaled molecular
partial volume (3DRISM-UC, Palmer et al., <i>J. Phys.: Condens.
Matter</i> <b>2010</b>, <i>22</i>, 492101). A
fast multigrid algorithm is the core of the method because it helps
to reduce the high computational costs associated with solving the
3DRISM equations. To facilitate future applications of the method,
we performed benchmarking of the algorithm on a set of several model
solutes in order to find optimal grid parameters and to test the performance
and accuracy of the algorithm. We have shown that the proposed new
multigrid algorithm is on average 24 times faster than the simple
Picard method and at least 3.5 times faster than the MDIIS method
which is currently actively used by the 3DRISM community (e.g., the
MDIIS method has been recently implemented in a new 3DRISM implicit
solvent routine in the recent release of the AmberTools 1.4 molecular
modeling package (Luchko et al. <i>J. Chem. Theory Comput</i>. <b>2010</b>, <i>6</i>, 607–624). Then we
have benchmarked the multigrid algorithm with chosen optimal parameters
on a set of 99 organic compounds. We show that average computational
time required for one 3DRISM calculation is 3.5 min per a small organic
molecule (10–20 atoms) on a standard personal computer. We
also benchmarked predicted solvation free energy values for all of
the compounds in the set against the corresponding experimental data.
We show that by using the proposed multigrid algorithm and the 3DRISM-UC
model, it is possible to obtain good correlation between calculated
and experimental results for solvation free energies of aqueous solutions
of small organic compounds (correlation coefficient 0.97, root-mean-square
deviation <1 kcal/mol)
Accurate calculations of the hydration free energies of druglike molecules using the reference interaction site model
We report on the results of testing the reference interaction site model (RISM) for the estimation of the hydration free energy of druglike molecules. The optimum model was selected after testing of different RISM free energy expressions combined with different quantum mechanics and empirical force-field methods of structure optimization and atomic partial charge calculation. The final model gave a systematic error with a standard deviation of 2.6 kcal/mol for a test set of 31 molecules selected from the SAMPL1 blind challenge set [J. P. Guthrie, J. Phys. Chem. B 113, 4501 (2009)]. After parametrization of this model to include terms for the excluded volume and the number of atoms of different types in the molecule, the root mean squared error for a test set of 19 molecules was less than 1.2 kcal/mol
Accurate calculations of the hydration free energies of druglike molecules using the reference interaction site model
We report on the results of testing the reference interaction site model (RISM) for the estimation of the hydration free energy of druglike molecules. The optimum model was selected after testing of different RISM free energy expressions combined with different quantum mechanics and empirical force-field methods of structure optimization and atomic partial charge calculation. The final model gave a systematic error with a standard deviation of 2.6 kcal/mol for a test set of 31 molecules selected from the SAMPL1 blind challenge set [J. P. Guthrie, J. Phys. Chem. B 113, 4501 (2009)]. After parametrization of this model to include terms for the excluded volume and the number of atoms of different types in the molecule, the root mean squared error for a test set of 19 molecules was less than 1.2 kcal/mol
Reference interaction site model with structural descriptors correction as an efficient tool for hydration free energy predictions
This abstract discusses reference interaction site models with structural descriptors correction as an efficient tool for hydration free energy predictions
An accurate prediction of hydration free energies by combination of molecular integral equations theory with structural descriptors
In this work, we report a novel method for the estimation of the hydration free energy of organic molecules, the structural descriptors correction (SDC) model. The method is based on a combination of the reference interaction site model (RISM) with several empirical corrections. The model requires only a small number of chemical descriptors associated with the main features of the chemical structure of solutes: excluded volume, branch, double bond, benzene ring, hydroxyl group, halogen atom, aldehyde group, ketone group, ether group, and phenol fragment. The optimum model was selected after testing of different RISM free energy expressions on a training set of 65 molecules. We show that the correction parameters of the SDC model are transferable between different chemical classes, which allows one to cover a wide range of organic solutes. The new model substantially increases the accuracy of calculated HFEs by RISM giving the standard deviation of the error for a test set of 120 organic molecules around 1.2 kcal/mol
Accurate calculation of the hydration free energies of biologically active molecules using the reference interaction site model
Describes the accurate calculation of the hydration free energies of biologically active molecules using the reference interaction site model
Efficient predictions of physchem properties of biomolecules in aqueous solutions using the Reference Interaction Site Model
This abstract discusses efficient predictions of physchem properties of biomolecules in aqueous solutions using the Reference Interaction Site Model