Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II. Toward Massively Parallel Computations Using Smooth Particle Mesh Ewald

2015 ◽  
Vol 11 (6) ◽  
pp. 2589-2599 ◽  
Author(s):  
Louis Lagardère ◽  
Filippo Lipparini ◽  
Étienne Polack ◽  
Benjamin Stamm ◽  
Éric Cancès ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Parallel Computations ◽  
Massively Parallel ◽  
Polarization Energy ◽  
Particle Mesh Ewald

scholarly journals Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations

2014 ◽  
Vol 10 (4) ◽  
pp. 1638-1651 ◽  
Author(s):  
Filippo Lipparini ◽  
Louis Lagardère ◽  
Benjamin Stamm ◽  
Eric Cancès ◽  
Michael Schnieders ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Massively Parallel ◽  
Polarization Energy

Efficient Treatment of Fixed and Induced Dipolar Interactions

2000 ◽  
Vol 653 ◽  
Author(s):  
Celeste Sagui ◽  
Thoma Darden
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Lagrangian Formalism ◽  
Dipolar Interactions ◽  
Time Step ◽  
Efficient Treatment ◽  
Particle Mesh Ewald ◽  
Fixed Charges ◽  
Self Consistency ◽  
Induced Dipoles

AbstractFixed and induced point dipoles have been implemented in the Ewald and Particle-Mesh Ewald (PME) formalisms. During molecular dynamics (MD) the induced dipoles can be propagated along with the atomic positions either by interation to self-consistency at each time step, or by a Car-Parrinello (CP) technique using an extended Lagrangian formalism. The use of PME for electrostatics of fixed charges and induced dipoles together with a CP treatment of dipole propagation in MD simulations leads to a cost overhead of only 33% above that of MD simulations using standard PME with fixed charges, allowing the study of polarizability in largemacromolecular systems.

Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems

2019 ◽  
Author(s):  
Frédéric Célerse ◽  
Louis Lagardere ◽  
Étienne Derat ◽  
Jean-Philip Piquemal
Keyword(s):  
Molecular Dynamics ◽  
Parallel Implementation ◽  
Steered Molecular Dynamics ◽  
Massively Parallel

This paper is dedicated to the massively parallel implementation of Steered Molecular Dynamics in the Tinker-HP softwtare. It allows for direct comparisons of polarizable and non-polarizable simulations of realistic systems.

Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems

2019 ◽  
Author(s):  
Frédéric Célerse ◽  
Louis Lagardere ◽  
Étienne Derat ◽  
Jean-Philip Piquemal
Keyword(s):  
Molecular Dynamics ◽  
Parallel Implementation ◽  
Steered Molecular Dynamics ◽  
Massively Parallel

This paper is dedicated to the massively parallel implementation of Steered Molecular Dynamics in the Tinker-HP softwtare. It allows for direct comparisons of polarizable and non-polarizable simulations of realistic systems.

scholarly journals Car-Parrinello Molecular Dynamics on Massively Parallel Computers

ChemPhysChem ◽  
2005 ◽  
Vol 6 (9) ◽  
pp. 1788-1793 ◽  
Author(s):  
Jürg Hutter ◽  
Alessandro Curioni
Keyword(s):  
Molecular Dynamics ◽  
Parallel Computers ◽  
Massively Parallel ◽  
Massively Parallel Computers
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