Literature DB >> 26631661

An Efficient Real Space Multigrid QM/MM Electrostatic Coupling.

Teodoro Laino1, Fawzi Mohamed1, Alessandro Laio1, Michele Parrinello1.   

Abstract

A popular strategy for simulating large systems where quantum chemical effects are important is the use of mixed quantum mechanical/molecular mechanics methods (QM/MM). While the cost of solving the Schrödinger equation in the QM part is the bottleneck of these calculations, evaluating the Coulomb interaction between the QM and the MM part is surprisingly expensive. In fact it can be just as time-consuming as solving the QM part. We present here a novel real space multigrid approach that handles Coulomb interactions very effectively and implement it in the CP2K code. This novel scheme cuts the cost of this part of the calculation by 2 orders of magnitude. The method does not need very fine-tuning or adjustable parameters, and it is quite accurate, leading to a dynamics with very good energy conservation. We exemplify the validity of our algorithms with simulations of water and of a zwitterionic dipeptide solvated in water.

Entities:  

Year:  2005        PMID: 26631661     DOI: 10.1021/ct050123f

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  35 in total

1.  A new smoothing function to introduce long-range electrostatic effects in QM/MM calculations.

Authors:  Dong Fang; Robert E Duke; G Andrés Cisneros
Journal:  J Chem Phys       Date:  2015-07-28       Impact factor: 3.488

2.  On the active site of mononuclear B1 metallo β-lactamases: a computational study.

Authors:  Jacopo Sgrignani; Alessandra Magistrato; Matteo Dal Peraro; Alejandro J Vila; Paolo Carloni; Roberta Pierattelli
Journal:  J Comput Aided Mol Des       Date:  2012-04-25       Impact factor: 3.686

Review 3.  Classical electrostatics for biomolecular simulations.

Authors:  G Andrés Cisneros; Mikko Karttunen; Pengyu Ren; Celeste Sagui
Journal:  Chem Rev       Date:  2013-08-27       Impact factor: 60.622

4.  Multiscale Simulation Reveals Passive Proton Transport Through SERCA on the Microsecond Timescale.

Authors:  Chenghan Li; Zhi Yue; L Michel Espinoza-Fonseca; Gregory A Voth
Journal:  Biophys J       Date:  2020-08-06       Impact factor: 4.033

5.  Acid activation mechanism of the influenza A M2 proton channel.

Authors:  Ruibin Liang; Jessica M J Swanson; Jesper J Madsen; Mei Hong; William F DeGrado; Gregory A Voth
Journal:  Proc Natl Acad Sci U S A       Date:  2016-10-24       Impact factor: 11.205

6.  Local DNA dynamics shape mutational patterns of mononucleotide repeats in human genomes.

Authors:  Albino Bacolla; Xiao Zhu; Hanning Chen; Katy Howells; David N Cooper; Karen M Vasquez
Journal:  Nucleic Acids Res       Date:  2015-04-20       Impact factor: 16.971

7.  Electron Redistribution within the Nitrogenase Active Site FeMo-Cofactor During Reductive Elimination of H2 to Achieve N≡N Triple-Bond Activation.

Authors:  Dmitriy A Lukoyanov; Zhi-Yong Yang; Dennis R Dean; Lance C Seefeldt; Simone Raugei; Brian M Hoffman
Journal:  J Am Chem Soc       Date:  2020-12-16       Impact factor: 15.419

8.  QM/MM metadynamics study of the direct decarboxylation mechanism for orotidine-5'-monophosphate decarboxylase using two different QM regions: acceleration too small to explain rate of enzyme catalysis.

Authors:  Courtney L Stanton; I-Feng W Kuo; Christopher J Mundy; Teodoro Laino; K N Houk
Journal:  J Phys Chem B       Date:  2007-10-10       Impact factor: 2.991

9.  Fragment-based Quantum Mechanical/Molecular Mechanical Simulations of Thermodynamic and Kinetic Process of the Ru2+-Ru3+ Self-Exchange Electron Transfer.

Authors:  Xiancheng Zeng; Xiangqian Hu; Weitao Yang
Journal:  J Chem Theory Comput       Date:  2012-12-11       Impact factor: 6.006

10.  Exploring structural and optical properties of fluorescent proteins by squeezing: modeling high-pressure effects on the mStrawberry and mCherry red fluorescent proteins.

Authors:  Adele D Laurent; Vladimir A Mironov; Prem P Chapagain; Alexander V Nemukhin; Anna I Krylov
Journal:  J Phys Chem B       Date:  2012-10-05       Impact factor: 2.991

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