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Development of Polarizable Models for Molecular Mechanical Calculations. 4. van der Waals Parametrization
journal contribution
posted on 2012-06-21, 00:00 authored by Junmei Wang, Piotr Cieplak, Jie Li, Qin Cai, Meng-Juei Hsieh, Ray Luo, Yong DuanIn the previous publications of this series, we presented
a set
of Thole induced dipole interaction models using four types of screening
functions. In this work, we document our effort to refine the van
der Waals parameters for the Thole polarizable models. Following the
philosophy of AMBER force field development, the van der Waals (vdW)
parameters were tuned for the Thole model with linear screening function
to reproduce both the ab initio interaction energies
and the experimental densities of pure liquids. An in-house genetic
algorithm was applied to maximize the fitness of “chromosomes”
which is a function of the root-mean-square errors (RMSE) of interaction
energy and liquid density. To efficiently explore the vdW parameter
space, a novel approach was developed to estimate the liquid densities
for a given vdW parameter set using the mean residue–residue
interaction energies through interpolation/extrapolation. This approach
allowed the costly molecular dynamics simulations be performed at
the end of each optimization cycle only and eliminated the simulations
during the cycle. Test results show notable improvements over the
original AMBER FF99 vdW parameter set, as indicated by the reduction
in errors of the calculated pure liquid densities (d), heats of vaporization (Hvap), and
hydration energies. The average percent error (APE) of the densities
of 59 pure liquids was reduced from 5.33 to 2.97%; the RMSE of Hvap was reduced from 1.98 to 1.38 kcal/mol;
the RMSE of solvation free energies of 15 compounds was reduced from
1.56 to 1.38 kcal/mol. For the interaction energies of 1639 dimers,
the overall performance of the optimized vdW set is slightly better
than the original FF99 vdW set (RMSE of 1.56 versus 1.63 kcal/mol).
The optimized vdW parameter set was also evaluated for the exponential
screening function used in the Amoeba force field to assess its applicability
for different types of screening functions. Encouragingly, comparable
performance was observed when the optimized vdW set was combined with
the Thole Amoeba-like polarizable model, particularly for the interaction
energy and liquid density calculations. Thus, the optimized vdW set
is applicable to both types of Thole models with either linear or
Amoeba-like screening functions.
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densityoptimized vdWAPEvan der Waalsab initio interaction energiesAMBER force field developmentoptimized vdW parameterAMBER FF 99 vdW parametervan der Waals parameters4. van der Waals ParametrizationIntest results showFF 99 vdWAmoeba force fieldThole polarizable modelsscreening functionRMSEscreening functionsinteraction energyvdW parameter spaceMolecular Mechanical Calculations
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