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

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• 作者：Shingo Ito^a ; Stephan Irle^b ; ^c ; ^d ; Yuko Okamoto^a ; ^d ; ^e ; ^f ; ^g ; ^{okamoto@phys.nagoya-u.ac.jp" class="auth_mail" title="E-mail the corresponding author}
• 关键词：Replica-exchange molecular dynamics ; Multidimensional replica-exchange method ; Umbrella sampling ; Replica-exchange umbrella sampling ; Density functional tight binding ; DFTB++ ; Malonaldehyde ; Phthalocyanine
• 刊名：Computer Physics Communications
• 出版年：2016
• 出版时间：July 2016
• 年：2016
• 卷：204
• 期：Complete
• 页码：1-10
• 全文大小：3104 K

文摘

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.