Chemical Effects on the Adhesion and Friction between Alkanethiol Monolayers:  Molecular Dynamics Simulations

Langmuir ◽  
2003 ◽  
Vol 19 (22) ◽  
pp. 9239-9245 ◽  
Author(s):  
Byeongwon Park ◽  
Michael Chandross ◽  
Mark J. Stevens ◽  
Gary S. Grest
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chemical Effects ◽  
Dynamics Simulations

scholarly journals Improvement of Performance, Stability and Continuity by Modified Size-Consistent Multipartitioning Quantum Mechanical/Molecular Mechanical Method

Molecules ◽  
2018 ◽  
Vol 23 (8) ◽  
pp. 1882 ◽  
Author(s):  
Hiroshi Watanabe
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Quantum Chemical ◽  
Quantum Mechanical ◽  
Mechanical Method ◽  
Chemical Effects ◽  
Temporal And Spatial ◽  
Dynamics Simulations ◽  
Spatial Discontinuity ◽  
Condensed Systems

For condensed systems, the incorporation of quantum chemical solvent effects into molecular dynamics simulations has been a major concern. To this end, quantum mechanical/molecular mechanical (QM/MM) techniques are popular and powerful options to treat gigantic systems. However, they cannot be directly applied because of temporal and spatial discontinuity problems. To overcome these problems, in a previous study, we proposed a corrective QM/MM method, size-consistent multipartitioning (SCMP) QM/MM and successfully demonstrated that, using SCMP, it is possible to perform stable molecular dynamics simulations by effectively taking into account solvent quantum chemical effects. The SCMP method is characterized by two original features: size-consistency of a QM region among all QM/MM partitioning and partitioning update. However, in our previous study, the performance was not fully elicited compared to the theoretical upper bound and the optimal partitioning update protocol and parameters were not fully verified. To elicit the potential performance, in the present study, we simplified the theoretical framework and modified the partitioning protocol.

scholarly journals Improvement of Performance, Stability, and Continuity by Modified Size-Consistent Multipartitioning QM/MM Method

2018 ◽  
Author(s):  
Hiroshi C. Watanabe
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Quantum Chemical ◽  
Quantum Mechanical ◽  
Size Consistency ◽  
Chemical Effects ◽  
Temporal And Spatial ◽  
Dynamics Simulations ◽  
Spatial Discontinuity ◽  
Condensed Systems

For condensed systems, the incorporation of quantum chemical solvent effects into molecular dynamics simulations has been a major concern. To this end, quantum mechanical/molecular mechanical (QM/MM) techniques are popular and powerful options to treat gigantic systems. However, they cannot be directly applied because of temporal and spatial discontinuity problems. To overcome these problems, in a previous study, we proposed a corrective QM/MM method, size-consistent multipartitioning (SCMP) QM/MM, and successfully demonstrated that, using SCMP, it is possible to perform stable molecular dynamics simulations by effectively taking into account solvent quantum chemical effects. The SCMP method is characterized by two original features: size-consistency of a QM region among all QM/MM partitioning and partitioning update. However, in our previous study, the performance was not fully elicited compared to the theoretical upper bound, and the optimal partitioning update protocol and parameters were not fully verified. To elicit the potential performance, in the present study, we simplified the theoretical framework and modified the partitioning protocol.

Nonequilibrium Chemical Effects in Single-Molecule SERS Revealed by Ab Initio Molecular Dynamics Simulations

2017 ◽  
Vol 121 (6) ◽  
pp. 1344-1350 ◽  
Author(s):  
Sean A. Fischer ◽  
Edoardo Aprà ◽  
Niranjan Govind ◽  
Wayne P. Hess ◽  
Patrick Z. El-Khoury
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Single Molecule ◽  
Ab Initio Molecular Dynamics ◽  
Chemical Effects ◽  
Dynamics Simulations
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