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Development of polarizable models for molecular mechanical calculations. 3. Polarizable water models conforming to Thole polarization screening schemes.

ABSTRACT: As an integrated step toward a coherent polarizable force field for biomolecular modeling, we analyzed four polarizable water models to evaluate their consistencies with the Thole polarization screening schemes utilized in our latest Amber polarizable force field. Specifically, we studied the performance of both the Thole linear and exponential schemes in these water models to assess their abilities to reproduce experimental water properties. The analysis shows that the tested water models reproduce most of the room-temperature properties of liquid water reasonably well but fall short of reproducing the dynamic properties and temperature-dependent properties. This study demonstrates the necessity to further fine-tune water polarizable potentials for more robust polarizable force fields for biomolecular simulations.

SUBMITTER: Wang J

PROVIDER: S-EPMC3493849 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature

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Development of polarizable models for molecular mechanical calculations. 3. Polarizable water models conforming to Thole polarization screening schemes.

Wang Jun J Cieplak Piotr P Cai Qin Q Hsieh Meng-Juei MJ Wang Junmei J Duan Yong Y Luo Ray R

The journal of physical chemistry. B 20120705 28

As an integrated step toward a coherent polarizable force field for biomolecular modeling, we analyzed four polarizable water models to evaluate their consistencies with the Thole polarization screening schemes utilized in our latest Amber polarizable force field. Specifically, we studied the performance of both the Thole linear and exponential schemes in these water models to assess their abilities to reproduce experimental water properties. The analysis shows that the tested water models repro ...[more]

PMID: 22712654

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Project description:In 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 (H(vap)), 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 H(vap) 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.

Project description:In the companion paper, we presented a set of induced dipole interaction models using four types of screening functions, which include the Applequist (no screening), the Thole linear, the Thole exponential model, and the Thole Tinker-like (another form of exponential screening function) functions. In this work, we evaluate the performance of polarizability models using a large set of amino acid analog pairs in conformations that are frequently observed in protein structures as a benchmark. For each amino acid pair, we calculated quantum mechanical interaction energies at the MP2/aug-cc-pVTZ//MP2/6-311++G(d,p) level with the basis set superposition error (BSSE) correction and compared them with molecular mechanics results. Encouragingly, all polarizable models significantly outperform the additive F94 and F03 models (mimicking AMBER ff94/ff99 and ff03 force fields, respectively) in reproducing the BSSE-corrected quantum mechanical interaction energies. In particular, the root-mean-square errors (RMSEs) for three Thole models in Set A (where the 1-2 and 1-3 interactions are turned off and all 1-4 interactions are included) are 1.456, 1.417, and 1.406 kcal/mol for model AL (Thole Linear), model AE (Thole exponential), and model AT (Thole Tinker-like), respectively. In contrast, the RMSEs are 3.729 and 3.433 kcal/mol for F94 and F03 models, respectively. A similar trend was observed for the average unsigned errors (AUEs), which are 1.057, 1.025, 1.011, 2.219, and 2.070 kcal/mol for AL, AE, AT, F94/ff99, and F03, respectively. Analyses based on the trend line slopes indicate that the two fixed charge models substantially underestimate the relative strengths of noncharge-charge interactions by 24 (F03) and 35% (F94), respectively, whereas the four polarizable models overestimate the relative strengths by 5 (AT), 3 (AL, AE), and 13% (AA), respectively. Agreement was further improved by adjusting the van der Waals parameters. Judging from the notably improved accuracy in comparison with the fixed charge models, the polarizable models are expected to form the foundation for the development of high quality polarizable force fields for protein and nucleic acid simulations.

Project description:A set of atomic polarizability parameters for a new polarizable Gaussian model (pGM) has been developed with the goal to accurately reproduce the polarizability anisotropy, taking advantage of its ability to attenuate all short-range electrostatic interactions, by fitting the ab initio molecular polarizability tensors ( A pq) calculated at the B3LYP/aug-cc-pVTZ level. For comparison, we also rederived the parameters for three Thole models in which the 1-2 (bonded), 1-3 (separated by two bonds), and 1-4 (separated by three bonds) interactions are fully included. The average percent errors (APEs) of molecular polarizability tensors for 4842 molecules or dimers are 2.98, 3.76, 3.28, and 3.82% for the pGM, Thole linear, Thole exponential, and Thole Amoeba models, respectively, with atom-type independent, universal screening factors (USF). The APEs are reduced further to 2.30, 2.69, 2.25, and 2.48% for the four corresponding polarizable models with atom-type dependent, variable screening factors (VSF). It is encouraging that the pGM with variable screening factors achieved APEs of 1.83 for 1155 amino acid analogs, dipeptides, and tetrapeptides, 1.39 for 28 nucleic acid bases, 0.708 for 1464 water clusters, and 1.99 for 85 dimers of water and biological building blocks. Compared to the new set of models, the APEs of the old Thole models that were fitted to isotropic molecular polarizabilities are 8.7% for set A (without the 1-2 and 1-3 interactions) and 6.3% for set D (with the 1-2 and 1-3 interactions) models, respectively. MPAD, a metric of molecular polarization anisotropy difference based on the diagonal terms of molecular polarizability tensors was defined and applied to assess the polarizable models in reproducing the ab initio molecular polarization anisotropy. The MPADs are 3.71, 4.70, 4.11, and 4.77% for the pGM, Thole linear, Thole exponential, and Thole Amoeba USF models, respectively. The APEs are reduced further to 2.85, 3.58, 2.90, and 3.15% for the four corresponding VSF models. Thus, the new pGM and Thole models notably improve molecular polarization anisotropy. Since pGM attenuates all short-range electrostatic interactions, its application is expected to improve stability in charge fitting, energy, and force calculations and the accuracy of multibody polarization.

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Development of polarizable models for molecular mechanical calculations. 3. Polarizable water models conforming to Thole polarization screening schemes.

Publications

Development of polarizable models for molecular mechanical calculations. 3. Polarizable water models conforming to Thole polarization screening schemes.

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