3DRISM Multigrid Algorithm
for Fast Solvation Free
Energy Calculations
- Publication date
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Abstract
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>, 607β624). 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 (10β20 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)