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Coarse-Graining ddCOSMO through an Interface between Tinker and the ddX Library.

ABSTRACT: The domain decomposition conductor-like screening model is an efficient way to compute the solvation energy of solutes within a polarizable continuum medium in a linear scaling computational time. Despite its efficiency, the application to very large systems is still challenging. A possibility to further accelerate the algorithm is resorting to coarse-graining strategies. In this paper we present a preliminary interface between the molecular dynamics package Tinker and the ddX library. The interface was used to test a united atom coarse-graining strategy that allowed us to push ddCOSMO to its limits by computing solvation energies on systems with up to 7 million atoms. We first present benchmarks to find an optimal discretization, and then, we discuss the performance and results obtained with fine- and coarse-grained solvation energy calculations.

SUBMITTER: Nottoli M

PROVIDER: S-EPMC9639080 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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Coarse-Graining ddCOSMO through an Interface between Tinker and the ddX Library.

Nottoli Michele M Mikhalev Aleksandr A Stamm Benjamin B Lipparini Filippo F

The journal of physical chemistry. B 20221020 43

The domain decomposition conductor-like screening model is an efficient way to compute the solvation energy of solutes within a polarizable continuum medium in a linear scaling computational time. Despite its efficiency, the application to very large systems is still challenging. A possibility to further accelerate the algorithm is resorting to coarse-graining strategies. In this paper we present a preliminary interface between the molecular dynamics package Tinker and the ddX library. The inter ...[more]

PMID: 36265187

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Dataset Information

Coarse-Graining ddCOSMO through an Interface between Tinker and the ddX Library.

Publications

Coarse-Graining ddCOSMO through an Interface between Tinker and the ddX Library.

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