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pyEFP: Automatic decomposition of the complex molecular systems into rigid polarizable fragments
Author(s) -
Odinokov Alexey V.,
Dubinets Nikita O.,
Bagaturyants Alexander A.
Publication year - 2018
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.25149
Subject(s) - merge (version control) , python (programming language) , computer science , fragment (logic) , ab initio , polarizability , decomposition , computational science , computational chemistry , chemistry , algorithm , molecule , information retrieval , programming language , organic chemistry
We present an open source tool able to describe intermolecular electrostatic interactions within the framework of the effective fragment potential (EFP) method. Complex molecular structure is subdivided into compact rigid fragments and parameters of their interactions are obtained from ab initio calculations. Automatic procedure allows for searching of these parameters into the existing database and merge new fragments into it. A set of standard fragments useful for the studies of organic semiconductors is also provided. Input files both for purely EFP and hybrid QM/MM calculations can be generated. The program is written in python and freely available on GitHub: https://github.com/ale-odinokov/pyEFP © 2017 Wiley Periodicals, Inc.