A Modified Divide-and-Conquer Linear-Scaling Quantum Force Field with Multipolar Charge Densities

2016 ◽  
pp. 21-50 ◽  
Keyword(s):  
Force Field ◽  
Divide And Conquer ◽  
Linear Scaling ◽  
Charge Densities ◽  
Quantum Force

scholarly journals Recent Advances toward a General Purpose Linear-Scaling Quantum Force Field

2014 ◽  
Vol 47 (9) ◽  
pp. 2812-2820 ◽  
Author(s):  
Timothy J. Giese ◽  
Ming Huang ◽  
Haoyuan Chen ◽  
Darrin M. York
Keyword(s):  
Force Field ◽  
General Purpose ◽  
Linear Scaling ◽  
Recent Advances ◽  
Quantum Force

scholarly journals Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions

2014 ◽  
Vol 10 (3) ◽  
pp. 1086-1098 ◽  
Author(s):  
Timothy J. Giese ◽  
Haoyuan Chen ◽  
Ming Huang ◽  
Darrin M. York
Keyword(s):  
Force Field ◽  
Noncovalent Interactions ◽  
Linear Scaling ◽  
Quantum Force

scholarly journals Combining experimental and simulation data of molecular processes via augmented Markov models

2017 ◽  
Vol 114 (31) ◽  
pp. 8265-8270 ◽  
Author(s):  
Simon Olsson ◽  
Hao Wu ◽  
Fabian Paul ◽  
Cecilia Clementi ◽  
Frank Noé
Keyword(s):  
Force Field ◽  
Structural Changes ◽  
Markov Models ◽  
Force Fields ◽  
Divide And Conquer ◽  
Simulation Data ◽  
Wide Range ◽  
Simulation And Experiment ◽  
Kinetics Of

Accurate mechanistic description of structural changes in biomolecules is an increasingly important topic in structural and chemical biology. Markov models have emerged as a powerful way to approximate the molecular kinetics of large biomolecules while keeping full structural resolution in a divide-and-conquer fashion. However, the accuracy of these models is limited by that of the force fields used to generate the underlying molecular dynamics (MD) simulation data. Whereas the quality of classical MD force fields has improved significantly in recent years, remaining errors in the Boltzmann weights are still on the order of a few kT, which may lead to significant discrepancies when comparing to experimentally measured rates or state populations. Here we take the view that simulations using a sufficiently good force-field sample conformations that are valid but have inaccurate weights, yet these weights may be made accurate by incorporating experimental data a posteriori. To do so, we propose augmented Markov models (AMMs), an approach that combines concepts from probability theory and information theory to consistently treat systematic force-field error and statistical errors in simulation and experiment. Our results demonstrate that AMMs can reconcile conflicting results for protein mechanisms obtained by different force fields and correct for a wide range of stationary and dynamical observables even when only equilibrium measurements are incorporated into the estimation process. This approach constitutes a unique avenue to combine experiment and computation into integrative models of biomolecular structure and dynamics.

Fast Electrostatic Force and Moment Calculations in Multibody-Based Simulations of Coarse-Grained Biopolymers

2011 ◽  
Author(s):  
Mohammad Poursina ◽  
Jeremy Laflin ◽  
Kurt S. Anderson
Keyword(s):  
Force Field ◽  
Long Range ◽  
Electrostatic Force ◽  
Center Of Mass ◽  
Computational Cost ◽  
Field Approximation ◽  
The Body ◽  
Divide And Conquer ◽  
Coarse Grained ◽  
Coarse Grain

In molecular simulations, the dominant portion of the computational cost is associated with force field calculations. Herein, we extend the approach used to approximate long range gravitational force and the associated moment in spacecraft dynamics to the coulomb forces present in coarse grained biopolymer simulations. We approximate the resultant force and moment for long-range particle-body and body-body interactions due to the electrostatic force field. The resultant moment approximated here is due to the fact that the net force does not necessarily act through the center of mass of the body (pseudoatom). This moment is considered in multibody-based coarse grain simulations while neglected in bead models which use particle dynamics to address the dynamics of the system. A novel binary divide and conquer algorithm (BDCA) is presented to implement the force field approximation. The proposed algorithm is implemented by considering each rigid/flexible domain as a node of the leaf level of the binary tree. This substructuring strategy is well suited to coarse grain simulations of chain biopolymers using an articulated multibody approach.

scholarly journals A first step towards quantum energy potentials of electron pairs

2019 ◽  
Vol 21 (8) ◽  
pp. 4215-4223 ◽  
Author(s):  
Julen Munárriz ◽  
Rubén Laplaza ◽  
A. Martín Pendás ◽  
Julia Contreras-García
Keyword(s):  
Force Field ◽  
Electron Pairs ◽  
Quantum Energy ◽  
Quantum Force

A first step towards the construction of a quantum force field for electron pairs in direct space is taken.

Derivation of Class II Force Fields. III. Characterization of a Quantum Force Field for Alkanes

1994 ◽  
Vol 34 (2) ◽  
pp. 195-231 ◽  
Author(s):  
J.R. Maple ◽  
M.-J. Hwang ◽  
T.P. Stockfisch ◽  
A.T. Hagler
Keyword(s):  
Force Field ◽  
Force Fields ◽  
Class Ii ◽  
Quantum Force

Derivation of class II force fields: V. Quantum force field for amides, peptides, and related compounds

1998 ◽  
Vol 19 (4) ◽  
pp. 430-458 ◽  
Author(s):  
J. R. Maple ◽  
M.-J. Hwang ◽  
K. J. Jalkanen ◽  
T. P. Stockfisch ◽  
A. T. Hagler
Keyword(s):  
Force Field ◽  
Force Fields ◽  
Class Ii ◽  
Quantum Force ◽  
Related Compounds
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