Time reversible and symplectic integrators for molecular dynamics simulations of rigid molecules

Kamberaj, Hiqmet; Low, Robert J.; Neal, Maureen P.

doi:10.1063/1.1906216

Cited by 167 publications

(150 citation statements)

References 45 publications

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“…This potential has a simple form of i=1,2 1/r 12 i with r i as the distance between the center of mass of each base pair and the ith rigid wall. The equations of motion for each base pair are integrated via a symplectic algorithm [13] and the Nose-Hoover chain thermostat is used to achieve the canonical ensemble at room temperature. After giving enough time for relaxation, we generated an ensemble of two-dimensionally confined DNA molecules.…”

Section: Methodsmentioning

confidence: 99%

Definition of the persistence length in the coarse-grained models of DNA elasticity

2012

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By considering the detailed structure of DNA in the base pair level, two possible definitions of the persistence length are compared. One definition is related to the orientation of the terminal base pairs, and the other is based on the vectors which connect two adjacent base pairs at each end of the molecule. It is shown that although these definitions approach each other for long DNA molecules, they are dramatically different on short length scales. We show analytically that the difference mostly comes from the shear flexibility of the molecule and can be used to measure the shear modulus of DNA.

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Section: Methodsmentioning

confidence: 99%

Definition of the persistence length in the coarse-grained models of DNA elasticity

2012

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“…The simulations were performed in the canonical (NVT) ensemble, in which translational and rotational degrees of freedom of rigid bodies were both thermostated using the Nose-Hoover algorithm with chains, as described by Hoover [54] and Martyna et al [55,56]; the rigid-body algorithm for NVT integration is explained elsewhere [57]. A Verlet time integrator was utilized with time step equal to 1 fs.…”

Section: Modelling Gas Adsorption and Simulation Of Internal Energy Bmentioning

confidence: 99%

Hybrid Reverse Monte Carlo simulation of amorphous carbon: Distinguishing between competing structures obtained using different modeling protocols

Farmahini

Bhatia

2015

Carbon

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Please cite this article as: Farmahini, A.H., Bhatia, S.K., Hybrid reverse monte carlo simulation of amorphous carbon: Distinguishing between competing structures obtained using different modelling protocols, Carbon (2014), doi: http://dx.doi.org/10.1016/j.carbon. 2014.11.013 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. ABSTRACTWe explore different multi-stage and multi-constraint modelling strategies using the Hybrid Reverse Monte Carlo (HRMC) technique to develop realistic models for the amorphous structure of silicon carbide derived-carbon, and investigate the effect of modelling parameters on the development of nano-structural features of the constructed models. It is shown that application of long simulations with slow thermal quench rate is essential for modelling of amorphous structures. Nevertheless, very slow quenching rates are shown to lead to the formation of configurations with large fraction of sp 2 carbon, lacking the level of disorder required to match structure-related experimental data. The predicted gas adsorption isotherms are very sensitive to the pore size distribution (PSD), thus the final structure must reasonably reproduce the total pore volume and pore size distribution of the experimental sample. The frequently-observed strong first peak of the DFT-based PSD obtained from argon adsorption is shown to be an artifact of argon inaccessibility. Pore accessibility analysis of the constructed models, as well as MD simulations of gas transport demonstrate that the HRMC constructed structures contain short-range structural anisotropy, however the models are successful in capturing the long range internal energy barriers of amorphous carbon for methane.

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“…al. 13 . The O-H bonds and H-O-H angles on the TIP4P-ice waters were constrained according to the SHAKE algorithm (convergence tolerance 1.0E-5 achieved over a maximum of 50 iterations).…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

An Inexpensive, Widely Available Material for 4 wt % Reversible Hydrogen Storage Near Room Temperature

Pascal

Boxe

Goddard

2011

J. Phys. Chem. Lett.

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Time reversible and symplectic integrators for molecular dynamics simulations of rigid molecules

Cited by 167 publications

References 45 publications

Definition of the persistence length in the coarse-grained models of DNA elasticity

Definition of the persistence length in the coarse-grained models of DNA elasticity

Hybrid Reverse Monte Carlo simulation of amorphous carbon: Distinguishing between competing structures obtained using different modeling protocols

An Inexpensive, Widely Available Material for 4 wt % Reversible Hydrogen Storage Near Room Temperature

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