scholarly journals Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields

2018 ◽  
Vol 9 (4) ◽  
pp. 956-972 ◽  
Author(s):  
Louis Lagardère ◽  
Luc-Henri Jolly ◽  
Filippo Lipparini ◽  
Félix Aviat ◽  
Benjamin Stamm ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Complex Systems ◽  
Force Fields ◽  
Massively Parallel ◽  
Multiscale Simulations ◽  
Point Dipole ◽  
Polarizable Force Fields ◽  
Large Complex ◽  
Parallel Software ◽  
Parallel Molecular Dynamics

Tinker-HP is massively parallel software dedicated to polarizable molecular dynamics.

scholarly journals Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems

2021 ◽  
Vol 17 (4) ◽  
pp. 2034-2053
Author(s):  
Olivier Adjoua ◽  
Louis Lagardère ◽  
Luc-Henri Jolly ◽  
Arnaud Durocher ◽  
Thibaut Very ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Complex Systems ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Point Dipole ◽  
Polarizable Force Fields ◽  
Large Complex ◽  
Dynamics Simulations

scholarly journals Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings

2019 ◽  
Vol 10 (30) ◽  
pp. 7200-7211 ◽  
Author(s):  
Daniele Loco ◽  
Louis Lagardère ◽  
Gérardo A. Cisneros ◽  
Giovanni Scalmani ◽  
Michael Frisch ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Complex Systems ◽  
Large Scale ◽  
Double Helix ◽  
Point Dipole ◽  
Thiazole Orange ◽  
Large Complex ◽  
Dna Double Helix

Hybrid DFT(Gaussian)/AMOEBA(Tinker/Tinker-HP) polarizable molecular dynamics including the QM/MM mutual polarization on large complex systems. Example of the thiazole orange dye buried in a DNA double helix, embedded in a sphere of water (16 500 atoms).

Unraveling interactions in large complex systems using quantum chemistry interpretative techniques and new generation polarizable force fields

2012 ◽  
Author(s):  
R. Chaudret ◽  
B. de Courcy ◽  
A. Marjolin ◽  
M.-C. van Severen ◽  
P. Y. Ren ◽  
...  
Keyword(s):  
Complex Systems ◽  
Quantum Chemistry ◽  
Force Fields ◽  
Polarizable Force Fields ◽  
Large Complex ◽  
New Generation

scholarly journals High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling

2021 ◽  
Author(s):  
Théo Jaffrelot Inizan ◽  
Frédéric Célerse ◽  
Olivier Adjoua ◽  
Dina El Ahdab ◽  
Luc-Henri Jolly ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Adaptive Sampling ◽  
Force Fields ◽  
Sampling Strategy ◽  
Md Simulations ◽  
Conformational Space ◽  
Many Body ◽  
Polarizable Force Fields ◽  
Main Protease

We provide an unsupervised adaptive sampling strategy capable of producing μs-timescale molecular dynamics (MD) simulations of large biosystems using many-body polarizable force fields (PFFs).

scholarly journals Investigating the Folding Dynamics of RNA Pseudoknot Structural Motif via Massively Parallel Molecular Dynamics

2014 ◽  
Vol 106 (2) ◽  
pp. 804a
Author(s):  
Amethyst Radcliffe ◽  
Samantha Cao ◽  
Benjamin Pham ◽  
Phuc La ◽  
Richard Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Motif ◽  
Massively Parallel ◽  
Folding Dynamics ◽  
Parallel Molecular Dynamics ◽  
Rna Pseudoknot

scholarly journals Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics

2010 ◽  
Vol 38 (14) ◽  
pp. 4856-4867 ◽  
Author(s):  
A. J. DePaul ◽  
E. J. Thompson ◽  
S. S. Patel ◽  
K. Haldeman ◽  
E. J. Sorin
Keyword(s):  
Molecular Dynamics ◽  
Conformational Dynamics ◽  
Massively Parallel ◽  
Parallel Molecular Dynamics

scholarly journals Static and Dynamic Properties of Curved Vapour-Liquid Interfaces by Massively Parallel Molecular Dynamics Simulation

2011 ◽  
pp. 73-84
Author(s):  
M. T. Horsch ◽  
S. K. Miroshnichenko ◽  
J. Vrabec ◽  
C. W. Glass ◽  
C. Niethammer ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamic Properties ◽  
Dynamics Simulation ◽  
Massively Parallel ◽  
Liquid Interfaces ◽  
Parallel Molecular Dynamics
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