Linearly scaling and almost Hamiltonian dielectric continuum molecular dynamics simulations through fast multipole expansions

2015 ◽  
Vol 143 (18) ◽  
pp. 184114 ◽  
Author(s):  
Konstantin Lorenzen ◽  
Gerald Mathias ◽  
Paul Tavan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Fast Multipole ◽  
Multipole Expansions ◽  
Dynamics Simulations ◽  
Dielectric Continuum

Molecular Dynamics Simulations of a Siloxane-Based Liquid Crystal Using an Improved Fast Multipole Algorithm Implementation

1995 ◽  
Vol 408 ◽  
Author(s):  
Alan McKenney ◽  
Ruth Pachter ◽  
Soumya Patnaik ◽  
Wade Adams
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Electrostatic Interactions ◽  
Liquid Crystalline ◽  
Molecular System ◽  
Dynamics Simulation ◽  
Molecular Cluster ◽  
Fast Multipole ◽  
Dynamics Simulations ◽  
Fast Multipole Algorithm

AbstractIn our continuing efforts towards designing materials with controlled optical properties, largescale molecular dynamics simulations of a molecular cluster of a liquid crystalline cyclic siloxane are still limited by the size of the molecular system. Such simulations enable evaluation of the orientation order parameter of the system, as well as modelling the behavior of the material in bulk. This study summarizes improvements in the implementation of the fast multipole algorithm for computing electrostatic interactions which is included in the molecular dynamics program PMD[7, 8], such as the elimination of computations for empty cells and the use of optimal interaction lists. Moreover, an improved implementation of a 3-D Fast Multipole Method (FMM3D) based on the algorithm previously proposed[1, 2] is described in detail. The structure of the module, details of the expansions, parallelization, and its integration with the molecular dynamics simulation code are explained in detail. Finally, the utility of this approach in the study of liquid crystalline materials is briefly illustrated.

Large Scale Molecular Dynamics Simulations of a Liquid Crystalline Droplet with Fast Multipole Implementations

1998 ◽  
Vol 538 ◽  
Author(s):  
Zhiqiang Wang ◽  
James Lupo ◽  
Soumya S. Patnaik ◽  
Alan McKenney ◽  
Ruth Pachter
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Electrostatic Interactions ◽  
Liquid Crystalline ◽  
Fast Multipole Method ◽  
Atomic Scale ◽  
Dynamics Simulation ◽  
Fast Multipole ◽  
Multipole Method ◽  
Dynamics Simulations

AbstractThe Fast Multipole Method (FMM) offers an efficient way (order O(N)) to handle long range electrostatic interactions, thus enabling more realistic molecular dynamics simulations of large molecular systems. The performance of the fast molecular dynamics (FMD) code, a parallel MD code being developed in our group, using the three-dimensional fast multipole method, shows a good speedup. The application to the full atomic-scale molecular dynamics simulation of a liquid crystalline droplet of 4-n-pentyl-4'-cyanobiphenyl (5CB) molecules, of size 35,872 atoms, shows strong surface effects on various orientational order parameters.

Sign in / Sign up

Export Citation Format

Share Document