Literature DB >> 26596150

Reaction Ensemble Monte Carlo Simulation of Complex Molecular Systems.

Thomas W Rosch1, Edward J Maginn1.   

Abstract

Acceptance rules for reaction ensemble Monte Carlo (RxMC) simulations containing classically modeled atomistic degrees of freedom are derived for complex molecular systems where insertions and deletions are achieved gradually by utilizing the continuous fractional component (CFC) method. A self-consistent manner in which to utilize statistical mechanical data contained in ideal gas free energy parameters during RxMC moves is presented. The method is tested by applying it to two previously studied systems containing intramolecular degrees of freedom: the propene metathesis reaction and methyl-tert-butyl-ether (MTBE) synthesis. Quantitative agreement is found between the current results and those of Keil et al. (J. Chem. Phys. 2005, 122, 164705) for the propene metathesis reaction. Differences are observed between the equilibrium concentrations of the present study and those of Lísal et al. (AIChE J. 2000, 46, 866-875) for the MTBE reaction. It is shown that most of this difference can be attributed to an incorrect formulation of the Monte Carlo acceptance rule. Efficiency gains using CFC MC as opposed to single stage molecule insertions are presented.

Entities:  

Year:  2011        PMID: 26596150     DOI: 10.1021/ct100615j

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  6 in total

1.  Unfolding of the chromatin fiber driven by overexpression of noninteracting bridging factors.

Authors:  Isha Malhotra; Bernardo Oyarzún; Bortolo Matteo Mognetti
Journal:  Biophys J       Date:  2021-01-14       Impact factor: 4.033

2.  Efficient Application of Continuous Fractional Component Monte Carlo in the Reaction Ensemble.

Authors:  Ali Poursaeidesfahani; Remco Hens; Ahmadreza Rahbari; Mahinder Ramdin; David Dubbeldam; Thijs J H Vlugt
Journal:  J Chem Theory Comput       Date:  2017-08-07       Impact factor: 6.006

3.  Brick-CFCMC: Open Source Software for Monte Carlo Simulations of Phase and Reaction Equilibria Using the Continuous Fractional Component Method.

Authors:  Remco Hens; Ahmadreza Rahbari; Sebastián Caro-Ortiz; Noura Dawass; Máté Erdős; Ali Poursaeidesfahani; Hirad S Salehi; Alper T Celebi; Mahinder Ramdin; Othonas A Moultos; David Dubbeldam; Thijs J H Vlugt
Journal:  J Chem Inf Model       Date:  2020-04-21       Impact factor: 4.956

4.  Multiple Free Energy Calculations from Single State Point Continuous Fractional Component Monte Carlo Simulation Using Umbrella Sampling.

Authors:  Ahmadreza Rahbari; Remco Hens; Othonas A Moultos; David Dubbeldam; Thijs J H Vlugt
Journal:  J Chem Theory Comput       Date:  2020-02-12       Impact factor: 6.006

5.  Reactive Grand-Canonical Monte Carlo Simulations for Modeling Hydration of MgCl2.

Authors:  Koen Heijmans; Ionut C Tranca; Ming-Wen Chang; Thijs J H Vlugt; Silvia V Gaastra-Nedea; David M J Smeulders
Journal:  ACS Omega       Date:  2021-11-25

6.  Molecular Simulation of Chemical Reaction Equilibrium by Computationally Efficient Free Energy Minimization.

Authors:  William R Smith; Weikai Qi
Journal:  ACS Cent Sci       Date:  2018-08-23       Impact factor: 14.553

  6 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.