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Iterative solvers for empirical partial atomic charges: breaking the curse of cubic numerical complexityстатья Исследовательская статья
Статья опубликована в высокорейтинговом журнале
Информация о цитировании статьи получена из
Web of Science,
Scopus
Статья опубликована в журнале из списка Web of Science и/или Scopus
Дата последнего поиска статьи во внешних источниках: 13 июня 2019 г.
- Авторы: Shaymardanov Arslan, Shulga Dmitry A., Palyulin Vladimir A.
- Журнал: Journal of Chemical Information and Modeling
- Том: 59
- Номер: 4
- Год издания: 2019
- Издательство: American Chemical Society
- Местоположение издательства: United States
- Первая страница: 1434
- Последняя страница: 1443
- DOI: 10.1021/acs.jcim.8b00848
- Аннотация: Rational drug design involves a vast amount of computations to get thermodynamically reliable results and often relies on atomic charges as means to model electrostatic interactions within the system. Computational inefficiency often hampers the development of new and wider dissemination of the known methods, thus any source to speed up the calculations without a sacrifice in quality is warranted. At the heart of many empirical methods of calculating atomic charges is the solution of a system of linear algebraic equations (SLAE). The classical method of solving SLAE – the Gauss method – has in general case a cubic computational complexity. It is shown that the use of iterative methods for solving SLAE, characteristic to typical empirical atomic charge calculation methods, makes it possible to significantly reduce the amount of calculations and to obtain a computational complexity approaching a quadratic one. Despite this phenomenon is well known in numerical methods, iterative solvers surprisingly do not seem to have been systematically applied to calculation of atomic charges via empirical schemes. Another finding is the relative values of the matrix elements, determined by the physical grounds of the interactions within the empirical system, generally lead to SLAE’s with well-defined matrices, suited to use with iterative solvers to fasten computation compared to using the non-iterative solvers. This finding broadens the applicability range of atomic charges obtained with empirical methods for such cases as e.g. account of polarizability via “on-the-fly” recalculation of charges in changing surroundings within the force fields in molecular dynamics settings.
- Добавил в систему: Шульга Дмитрий Александрович