Implementation of replica-exchange umbrella sampling in the DFTB+ semiempirical quantum chemistry package

Shingo Ito; Stephan Irle; Yuko Okamoto

doi:10.1016/j.cpc.2016.02.010

Implementation of replica-exchange umbrella sampling in the DFTB+ semiempirical quantum chemistry package

Shingo Ito
, Stephan Irle
, Yuko Okamoto

Research output: Contribution to journal › Article › peer-review

6 Scopus citations

Abstract

The replica-exchange umbrella sampling (REUS) method combines replica-exchange and umbrella sampling methods and allows larger conformational sampling than conventional simulation methods. This method has been used in many studies to understand docking mechanisms and the functions of molecules. However, REUS has not been combined with quantum chemical codes. Therefore, we implemented the REUS simulation technique in the DFTB+ quantum chemistry code utilizing approximate density functional theory. We performed REUS simulations of an intra-molecular proton transfer reaction of malonaldehyde and a formation of a phthalocyanine from four phthalonitriles and one iron atom to validate the reliability of our implemented REUS-DFTB+ combination.

Original language	English
Pages (from-to)	1-10
Number of pages	10
Journal	Computer Physics Communications
Volume	204
DOIs	https://doi.org/10.1016/j.cpc.2016.02.010
State	Published - Jul 1 2016
Externally published	Yes

Funding

S.I. was supported by the Program for Leading Graduate Schools “Integrative Graduate Education and Research in Green Natural Sciences” of Nagoya University . Y.O. was supported, in part, by the JSPS Grants in Aid for Scientific Research (A) (No. 25247071 ), for Scientific Research on Innovative Areas (“Dynamical Ordering and Integrated Functions”), and for Computational Materials Science Initiative from MEXT , Japan.

Keywords

DFTB+
Density functional tight binding
Malonaldehyde
Multidimensional replica-exchange method
Phthalocyanine
Replica-exchange molecular dynamics
Replica-exchange umbrella sampling
Umbrella sampling

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10.1016/j.cpc.2016.02.010

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title = "Implementation of replica-exchange umbrella sampling in the DFTB+ semiempirical quantum chemistry package",

abstract = "The replica-exchange umbrella sampling (REUS) method combines replica-exchange and umbrella sampling methods and allows larger conformational sampling than conventional simulation methods. This method has been used in many studies to understand docking mechanisms and the functions of molecules. However, REUS has not been combined with quantum chemical codes. Therefore, we implemented the REUS simulation technique in the DFTB+ quantum chemistry code utilizing approximate density functional theory. We performed REUS simulations of an intra-molecular proton transfer reaction of malonaldehyde and a formation of a phthalocyanine from four phthalonitriles and one iron atom to validate the reliability of our implemented REUS-DFTB+ combination.",

keywords = "DFTB+, Density functional tight binding, Malonaldehyde, Multidimensional replica-exchange method, Phthalocyanine, Replica-exchange molecular dynamics, Replica-exchange umbrella sampling, Umbrella sampling",

author = "Shingo Ito and Stephan Irle and Yuko Okamoto",

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AU - Ito, Shingo

AU - Irle, Stephan

AU - Okamoto, Yuko

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N2 - The replica-exchange umbrella sampling (REUS) method combines replica-exchange and umbrella sampling methods and allows larger conformational sampling than conventional simulation methods. This method has been used in many studies to understand docking mechanisms and the functions of molecules. However, REUS has not been combined with quantum chemical codes. Therefore, we implemented the REUS simulation technique in the DFTB+ quantum chemistry code utilizing approximate density functional theory. We performed REUS simulations of an intra-molecular proton transfer reaction of malonaldehyde and a formation of a phthalocyanine from four phthalonitriles and one iron atom to validate the reliability of our implemented REUS-DFTB+ combination.

AB - The replica-exchange umbrella sampling (REUS) method combines replica-exchange and umbrella sampling methods and allows larger conformational sampling than conventional simulation methods. This method has been used in many studies to understand docking mechanisms and the functions of molecules. However, REUS has not been combined with quantum chemical codes. Therefore, we implemented the REUS simulation technique in the DFTB+ quantum chemistry code utilizing approximate density functional theory. We performed REUS simulations of an intra-molecular proton transfer reaction of malonaldehyde and a formation of a phthalocyanine from four phthalonitriles and one iron atom to validate the reliability of our implemented REUS-DFTB+ combination.

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KW - Density functional tight binding

KW - Malonaldehyde

KW - Multidimensional replica-exchange method

KW - Phthalocyanine

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KW - Replica-exchange umbrella sampling

KW - Umbrella sampling

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SP - 1

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JO - Computer Physics Communications

JF - Computer Physics Communications

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Implementation of replica-exchange umbrella sampling in the DFTB+ semiempirical quantum chemistry package

Abstract

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Keywords

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