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 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.

Molecular Dynamics Using Non-Variational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation and Application to the Bond Capacity Model

2019 ◽  
Author(s):  
Pier Paolo Poier ◽  
Louis Lagardere ◽  
Jean-Philip Piquemal ◽  
Frank Jensen
Keyword(s):  
Boundary Conditions ◽  
Periodic Boundary ◽  
Force Fields ◽  
Periodic Boundary Conditions ◽  
Computational Effort ◽  
Polarizable Force Fields ◽  
Energy Models ◽  
Capacity Model ◽  
Energy Gradient ◽  
Polarization Models

<div> <div> <div> <p>We extend the framework for polarizable force fields to include the case where the electrostatic multipoles are not determined by a variational minimization of the electrostatic energy. Such models formally require that the polarization response is calculated for all possible geometrical perturbations in order to obtain the energy gradient required for performing molecular dynamics simulations. </p><div> <div> <div> <p>By making use of a Lagrange formalism, however, this computational demanding task can be re- placed by solving a single equation similar to that for determining the electrostatic variables themselves. Using the recently proposed bond capacity model that describes molecular polarization at the charge-only level, we show that the energy gradient for non-variational energy models with periodic boundary conditions can be calculated with a computational effort similar to that for variational polarization models. The possibility of separating the equation for calculating the electrostatic variables from the energy expression depending on these variables without a large computational penalty provides flexibility in the design of new force fields. </p><div><div><div> </div> </div> </div> <p> </p><div> <div> <div> <p>variables themselves. Using the recently proposed bond capacity model that describes molecular polarization at the charge-only level, we show that the energy gradient for non-variational energy models with periodic boundary conditions can be calculated with a computational effort similar to that for variational polarization models. The possibility of separating the equation for calculating the electrostatic variables from the energy expression depending on these variables without a large computational penalty provides flexibility in the design of new force fields. </p> </div> </div> </div> </div> </div> </div> </div> </div> </div>

scholarly journals Nonlinearity-generated resilience in large complex systems

2021 ◽  
Vol 103 (2) ◽  
Author(s):  
S. Belga Fedeli ◽  
Y. V. Fyodorov ◽  
J. R. Ipsen
Keyword(s):  
Complex Systems ◽  
Large Complex

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).

Dynamic response of large complex systems

1960 ◽  
Vol 269 (4) ◽  
pp. 274-298
Author(s):  
Mihajlo D. Mesarović
Keyword(s):  
Dynamic Response ◽  
Complex Systems ◽  
Large Complex
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