Literature DB >> 26587597

Convergence of Sampling Kirkwood-Buff Integrals of Aqueous Solutions with Molecular Dynamics Simulations.

Pritam Ganguly1, Nico F A van der Vegt1.   

Abstract

We discuss two methods for calculating Kirkwood-Buff integrals (KBIs) of aqueous cosolvent solutions from molecular simulations. The first method is based on computing running integrals over radial distribution functions obtained from NVT or NpT simulations. The second, more recent method, originally introduced by Schnell et al. (J. Phys. Chem. B2011, 115, 10911), obtains the KBIs from direct analysis of particle number fluctuations in small, open subvolumes embedded in a larger reservoir as provided by the NVT (NpT) simulation cell. The thermodynamic limit is taken in the first method by using the plateau-values of the running KBIs for large distances, while in the second method an analytical finite-size scaling relation is applied to the KBIs of subvolumes of variable size. We find that direct analysis of particle number fluctuations at small scales provides more precise estimates of KBIs for methanol-water and urea-water solutions. Converged KBIs could, however, not be obtained from nanosecond time scale molecular dynamics simulations with either of the two methods. Based on 0.1 μs simulation trajectories of small and large system sizes time-converged KBIs were obtained with both methods. The running integral method suffers, however, from stronger finite-size artifacts than the sub-box method, also when empirical finite-size tail corrections are applied to the radial distribution functions.

Entities:  

Year:  2013        PMID: 26587597     DOI: 10.1021/ct301017q

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


  14 in total

1.  Kirkwood-Buff integrals for hard-core Yukawa fluids.

Authors:  Han-Fei Chen; Jiang-Tao Li; Fang Gu; Hai-Jun Wang
Journal:  Eur Phys J E Soft Matter       Date:  2017-11-03       Impact factor: 1.890

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Authors:  Michele Di Pierro; Mauro L Mugnai; Ron Elber
Journal:  J Phys Chem B       Date:  2014-08-08       Impact factor: 2.991

3.  Finite-Size Effects of Binary Mutual Diffusion Coefficients from Molecular Dynamics.

Authors:  Seyed Hossein Jamali; Ludger Wolff; Tim M Becker; André Bardow; Thijs J H Vlugt; Othonas A Moultos
Journal:  J Chem Theory Comput       Date:  2018-04-30       Impact factor: 6.006

4.  Kirkwood-Buff Integrals Using Molecular Simulation: Estimation of Surface Effects.

Authors:  Noura Dawass; Peter Krüger; Sondre K Schnell; Othonas A Moultos; Ioannis G Economou; Thijs J H Vlugt; Jean-Marc Simon
Journal:  Nanomaterials (Basel)       Date:  2020-04-16       Impact factor: 5.076

5.  Characterizing Polymer Hydration Shell Compressibilities with the Small-System Method.

Authors:  Madhusmita Tripathy; Swaminath Bharadwaj; Shadrack Jabes B; Nico F A van der Vegt
Journal:  Nanomaterials (Basel)       Date:  2020-07-25       Impact factor: 5.076

6.  Optimizing Nonbonded Interactions of the OPLS Force Field for Aqueous Solutions of Carbohydrates: How to Capture Both Thermodynamics and Dynamics.

Authors:  Seyed Hossein Jamali; Thijs van Westen; Othonas A Moultos; Thijs J H Vlugt
Journal:  J Chem Theory Comput       Date:  2018-11-20       Impact factor: 6.006

7.  Generalized Moment Correction for Long-Ranged Electrostatics.

Authors:  Björn Stenqvist; Vidar Aspelin; Mikael Lund
Journal:  J Chem Theory Comput       Date:  2020-05-07       Impact factor: 6.006

Review 8.  Fluctuations, Finite-Size Effects and the Thermodynamic Limit in Computer Simulations: Revisiting the Spatial Block Analysis Method.

Authors:  Maziar Heidari; Kurt Kremer; Raffaello Potestio; Robinson Cortes-Huerto
Journal:  Entropy (Basel)       Date:  2018-03-24       Impact factor: 2.524

9.  A Hybrid Monte Carlo Self-Consistent Field Model of Physical Gels of Telechelic Polymers.

Authors:  J Bergsma; F A M Leermakers; J M Kleijn; J van der Gucht
Journal:  J Chem Theory Comput       Date:  2018-11-12       Impact factor: 6.006

10.  Structural, Thermodynamic, and Transport Properties of Aqueous Reline and Ethaline Solutions from Molecular Dynamics Simulations.

Authors:  Alper T Celebi; Thijs J H Vlugt; Othonas A Moultos
Journal:  J Phys Chem B       Date:  2019-12-12       Impact factor: 2.991

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