Comment on "a minimal implementation of the AMBER-GAUSSIAN interface for Ab Initio QM/MM-MD simulation"

被引：2

作者：

Roberts, Benjamin P. ^{[1
,2
]}

Seabra, Gustavo M. ^{[3
]}

Roitberg, Adrian E. ^{[1
,2
]}

Merz, Kenneth M. ^{[1
,2
]}

Deumens, Erik ^{[1
,2
]}

Torras, Juan ^{[4
]}

Trickey, Samuel B. ^{[1
,2
]}

机构：

[1] Univ Florida, Dept Phys, Quantum Theory Project, Gainesville, FL 32611 USA

[2] Univ Florida, Dept Chem, Quantum Theory Project, Gainesville, FL 32611 USA

[3] Univ Fed Pernambuco, Dept Quim Fundamental, BR-50740540 Recife, PE, Brazil

[4] Univ Politecn Cataluna, EEI, Dept Engn Quim, Igualada 08700, Spain

来源：

JOURNAL OF COMPUTATIONAL CHEMISTRY | 2012年 / 33卷 / 19期

基金：

美国国家科学基金会;

关键词：

multiscale simulations; hybrid QM; MD or QM; MM simulations; AMBER-PUPIL-GAUSSIAN interface; PUPIL;

D O I：

10.1002/jcc.23003

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

We comment upon the recent critique of use of the Program for User Package Interfacing and Linking (PUPIL) system for linking AMBER and GAUSSIAN in a multiscale quantum mechanical/molecular mechanics (QM/MM) simulation (Okamoto et al., J. Comput. Chem. 2011, 32, 932). Specifically, their method for computing forces on the MM particles from the QM region via the GAUSSIAN-03 electrical field was already implemented in PUPIL version 1.3, publicly available beginning December 2009. Some other doubtful characterizations of PUPIL are discussed briefly in the context of current awareness of open-source codes more generally. (c) 2012 Wiley Periodicals, Inc.

引用

页码：1643 / 1644

页数：2

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