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.

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.

scholarly journals Formation Mechanism of Ion Channel in Channelrhodopsin-2: Molecular Dynamics Simulation and Steering Molecular Dynamics Simulations

2019 ◽  
Vol 20 (15) ◽  
pp. 3780 ◽  
Author(s):  
Ting Yang ◽  
Wenying Zhang ◽  
Jie Cheng ◽  
Yanhong Nie ◽  
Qi Xin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ion Channel ◽  
Molecular Dynamics Simulations ◽  
Formation Mechanism ◽  
Binding Sites ◽  
Electrostatic Interactions ◽  
Potential Of Mean Force ◽  
Dynamics Simulation ◽  
Cationic Channel ◽  
Dynamics Simulations

Channelrhodopsin-2 (ChR2) is a light-activated and non-selective cationic channel protein that can be easily expressed in specific neurons to control neuronal activity by light. Although ChR2 has been extensively used as an optogenetic tool in neuroscience research, the molecular mechanism of cation channel formation following retinal photoisomerization in ChR2 is not well understood. In this paper, studies of the closed and opened state ChR2 structures are presented. The formation of the cationic channel is elucidated in atomic detail using molecular dynamics simulations on the all-trans-retinal (ChR2-trans) configuration of ChR2 and its isomerization products, 13-cis-retinal (ChR2-cis) configuration, respectively. Photoisomerization of the retinal-chromophore causes the destruction of interactions among the crucial residues (e.g., E90, E82, N258, and R268) around the channel and the extended H-bond network mediated by numerous water molecules, which opens the pore. Steering molecular dynamics (SMD) simulations show that the electrostatic interactions at the binding sites in intracellular gate (ICG) and central gate (CG) can influence the transmembrane transport of Na+ in ChR2-cis obviously. Potential of mean force (PMF) constructed by SMD and umbrella sampling also found the existing energy wells at these two binding sites during the transportation of Na+. These wells partly hinder the penetration of Na+ into cytoplasm through the ion channel. This investigation provides a theoretical insight on the formation mechanism of ion channels and the mechanism of ion permeation.

scholarly journals Petascale molecular dynamics simulation using the fast multipole method on K computer

2014 ◽  
Vol 185 (10) ◽  
pp. 2575-2585 ◽  
Author(s):  
Yousuke Ohno ◽  
Rio Yokota ◽  
Hiroshi Koyama ◽  
Gentaro Morimoto ◽  
Aki Hasegawa ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Fast Multipole Method ◽  
Dynamics Simulation ◽  
Fast Multipole ◽  
Multipole Method
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