Determination of force field parameters for molecular simulation by molecular simulation: An application of the weak‐coupling method

1995 ◽  
Vol 102 (15) ◽  
pp. 6199-6207 ◽  
Author(s):  
Swie Lan Njo ◽  
Wilfred F. van Gunsteren ◽  
Florian Müller‐Plathe
Keyword(s):  
Force Field ◽  
Molecular Simulation ◽  
Weak Coupling ◽  
Coupling Method ◽  
Force Field Parameters ◽  
Weak Coupling Method

Development of a computer program for the determination of force field parameters derived from ab initio pes

1995 ◽  
Author(s):  
Ugo Cosentino ◽  
Giorgio Moro ◽  
Demetrio Pitea ◽  
Mercedes Procopio ◽  
Pier Carlo Fantucci
Keyword(s):  
Computer Program ◽  
Force Field ◽  
Ab Initio ◽  
Force Field Parameters

scholarly journals Development of Force Field Parameters for Molecular Simulation of Polylactide

2011 ◽  
Vol 7 (11) ◽  
pp. 3756-3767 ◽  
Author(s):  
James H. McAliley ◽  
David A. Bruce
Keyword(s):  
Force Field ◽  
Molecular Simulation ◽  
Force Field Parameters

scholarly journals Structural-Kinetic-Thermodynamic Relationships Identified from Physics-based Molecular Simulation Models

2017 ◽  
Author(s):  
Joseph F. Rudzinski ◽  
Tristan Bereau
Keyword(s):  
Thermodynamic Properties ◽  
Force Field ◽  
Molecular Simulation ◽  
Simulation Models ◽  
Coarse Grained ◽  
Kinetic Properties ◽  
Coarse Grained Model ◽  
Forbidden Configurations ◽  
Force Field Parameters ◽  
Representative System

Coarse-grained molecular simulation models have provided immense, often general, insight into the complex behavior of condensed-phase systems, but suffer from a lost connection to the true dynamical properties of the underlying system. In general, the physics that is built into a model shapes the free-energy landscape, restricting the attainable static and kinetic properties. In this work, we perform a detailed investigation into the property interrelationships resulting from these restrictions, for a representative system of the helix-coil transition. Inspired by high-throughput studies, we systematically vary force-field parameters and monitor their structural, kinetic, and thermodynamic properties. The focus of our investigation is a simple coarse-grained model, which accurately represents the underlying structural ensemble, i.e., effectively avoids sterically-forbidden configurations. As a result of this built-in physics, we observe a rather large restriction in the topology of the networks characterizing the simulation kinetics. When screening across force-field parameters, we find that structurally-accurate models also best reproduce the kinetics, suggesting structural-kinetic relationships for these models. Additionally, an investigation into thermodynamic properties reveals a link between the cooperativity of the transition and the network topology at a single reference temperature.

EXPERIMENTAL TRACKING OF UNSTABLE ORBITS IN DRIVEN DIODE RESONATOR BY WEAK COUPLING

1996 ◽  
Vol 06 (04) ◽  
pp. 769-774 ◽  
Author(s):  
JONG CHEOL SHIN ◽  
SOOK-IL KWUN ◽  
YOUNGTAE KIM
Keyword(s):  
Feedback Control ◽  
Weak Coupling ◽  
Control Parameter ◽  
Chaotic Regime ◽  
Coupling Method ◽  
Generic Properties ◽  
Wide Range ◽  
Resonator System ◽  
Weak Coupling Method

The weak coupling method is demonstrated to stabilize and track the unstable orbits in the diode resonator system. Continuous tracking of the unstable orbits could be achieved over a wide range from the periodic down to the deep chaotic regime as the control parameter is varied continuously without changing the feedback control parameter. During the tracking of unstable orbits, hysteresis as well as switching of the attractors are observed and these are supposed to be the generic properties of continuous tracking.

Development of Cu2+-Based Distance Methods and Force Field Parameters for the Determination of PNA Conformations and Dynamics by EPR and MD Simulations

2020 ◽  
Vol 124 (35) ◽  
pp. 7544-7556
Author(s):  
Austin Gamble Jarvi ◽  
Artur Sargun ◽  
Xiaowei Bogetti ◽  
Junmei Wang ◽  
Catalina Achim ◽  
...  
Keyword(s):  
Force Field ◽  
Md Simulations ◽  
Distance Methods ◽  
Force Field Parameters

Optimal determination of force field parameters for reduced molecular dynamics model

2019 ◽  
Vol 236 ◽  
pp. 86-94
Author(s):  
Hyun-Seok Kim ◽  
Jae-Hyun Kim ◽  
Song-Hyun Cha ◽  
Seonho Cho
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Dynamics Model ◽  
Force Field Parameters

Stability of Energy Transfer in the Weak Coupling Method

2008 ◽  
pp. 111-119
Author(s):  
Konstantin Fackeldey ◽  
Rolf Krause ◽  
Marc Alexander Schweitzer
Keyword(s):  
Energy Transfer ◽  
Weak Coupling ◽  
Coupling Method ◽  
Weak Coupling Method

scholarly journals Parametrization of stochastic multiscale triads

2016 ◽  
Author(s):  
Jeroen Wouters ◽  
Stamen I. Dolaptchiev ◽  
Valerio Lucarini ◽  
Ulrich Achatz
Keyword(s):  
Model Reduction ◽  
Weak Coupling ◽  
Degrees Of Freedom ◽  
Coupling Model ◽  
Linear Response Theory ◽  
Coupling Method ◽  
Scale Separation ◽  
Time Scale Separation ◽  
Weakly Coupled ◽  
Weak Coupling Method

Abstract. We discuss applications of a recently developed method for model reduction based on linear response theory of weakly coupled dynamical systems. We apply the weak coupling method to simple stochastic differential equations with slow and fast degrees of freedom. The weak coupling model reduction method results in general in a non-Markovian system, we therefore discuss the Markovianization of the system to allow for straightforward numerical integration. We compare the applied method to the equations obtained through homogenization in the limit of large time scale separation between slow and fast degrees of freedom. We numerically compare the ensemble spread from a fixed initial condition, correlation functions and exit times from a domain. The weak coupling method gives more accurate results in all test cases, albeit with a higher numerical cost.

A weak coupling method between the dynamics code HOST and the 3D unsteady Euler code WAVES

2001 ◽  
Vol 5 (6) ◽  
pp. 397-408 ◽  
Author(s):  
Gaëlle Servera ◽  
Philippe Beaumier ◽  
Michel Costes
Keyword(s):  
Weak Coupling ◽  
Coupling Method ◽  
Weak Coupling Method
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