Literature DB >> 29785645

Concurrent coupling of realistic and ideal models of liquids and solids in Hamiltonian adaptive resolution simulations.

Maziar Heidari1, Robinson Cortes-Huerto1, Kurt Kremer1, Raffaello Potestio2,3,4.   

Abstract

To understand the properties of a complex system it is often illuminating to perform a comparison with a simpler, even idealised one. A prototypical application of this approach is the calculation of free energies and chemical potentials in liquids, which can be decomposed in the sum of ideal and excess contributions. In the same spirit, in computer simulations it is possible to extract useful information on a given system making use of setups where two models, an accurate one and a simpler one, are concurrently employed and directly coupled. Here, we tackle the issue of coupling atomistic or, more in general, interacting models of a system with the corresponding idealised representations: for a liquid, this is the ideal gas, i.e. a collection of non-interacting particles; for a solid, we employ the ideal Einstein crystal, a construct in which particles are decoupled from one another and restrained by a harmonic, exactly integrable potential. We describe in detail the practical and technical aspects of these simulations, and suggest that the concurrent usage and coupling of realistic and ideal models represents a promising strategy to investigate liquids and solids in silico.

Keywords:  Topical issue: Advances in Computational Methods for Soft Matter Systems

Year:  2018        PMID: 29785645     DOI: 10.1140/epje/i2018-11675-x

Source DB:  PubMed          Journal:  Eur Phys J E Soft Matter        ISSN: 1292-8941            Impact factor:   1.890


  25 in total

1.  Molecular dynamics simulations of biomolecules.

Authors:  Martin Karplus
Journal:  Acc Chem Res       Date:  2002-06       Impact factor: 22.384

2.  Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models.

Authors:  Cristian Micheletti; Paolo Carloni; Amos Maritan
Journal:  Proteins       Date:  2004-05-15

3.  "Learn on the fly": a hybrid classical and quantum-mechanical molecular dynamics simulation.

Authors:  Gabor Csányi; T Albaret; M C Payne; A De Vita
Journal:  Phys Rev Lett       Date:  2004-10-19       Impact factor: 9.161

4.  Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics.

Authors:  Christopher J Fennell; J Daniel Gezelter
Journal:  J Chem Phys       Date:  2006-06-21       Impact factor: 3.488

5.  A macromolecule in a solvent: adaptive resolution molecular dynamics simulation.

Authors:  Matej Praprotnik; Luigi Delle Site; Kurt Kremer
Journal:  J Chem Phys       Date:  2007-04-07       Impact factor: 3.488

6.  Using force-based adaptive resolution simulations to calculate solvation free energies of amino acid sidechain analogues.

Authors:  Raffaele Fiorentini; Kurt Kremer; Raffaello Potestio; Aoife C Fogarty
Journal:  J Chem Phys       Date:  2017-06-28       Impact factor: 3.488

7.  Hamiltonian adaptive resolution simulation for molecular liquids.

Authors:  Raffaello Potestio; Sebastian Fritsch; Pep Español; Rafael Delgado-Buscalioni; Kurt Kremer; Ralf Everaers; Davide Donadio
Journal:  Phys Rev Lett       Date:  2013-03-05       Impact factor: 9.161

8.  Adaptive Resolution Simulations with Self-Adjusting High-Resolution Regions.

Authors:  Karsten Kreis; Raffaello Potestio; Kurt Kremer; Aoife C Fogarty
Journal:  J Chem Theory Comput       Date:  2016-07-20       Impact factor: 6.006

9.  Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme.

Authors:  Thomas Tarenzi; Vania Calandrini; Raffaello Potestio; Alejandro Giorgetti; Paolo Carloni
Journal:  J Chem Theory Comput       Date:  2017-10-27       Impact factor: 6.006

10.  Protein structural fluctuations during a period of 100 ps.

Authors:  M Karplus; J A McCammon
Journal:  Nature       Date:  1979-02-15       Impact factor: 49.962

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  4 in total

1.  Topical Issue on Advances in Computational Methods for Soft Matter Systems.

Authors:  Lorenzo Rovigatti; Flavio Romano; John Russo
Journal:  Eur Phys J E Soft Matter       Date:  2018-08-29       Impact factor: 1.890

2.  Topical Issue on Dielectric Spectroscopy Applied to Soft Matter.

Authors:  Simone Napolitano
Journal:  Eur Phys J E Soft Matter       Date:  2020-01-23       Impact factor: 1.890

3.  SAMPL7 TrimerTrip host-guest binding poses and binding affinities from spherical-coordinates-biased simulations.

Authors:  Zhaoxi Sun
Journal:  J Comput Aided Mol Des       Date:  2020-08-10       Impact factor: 3.686

Review 4.  From adaptive resolution to molecular dynamics of open systems.

Authors:  Robinson Cortes-Huerto; Matej Praprotnik; Kurt Kremer; Luigi Delle Site
Journal:  Eur Phys J B       Date:  2021-09-23       Impact factor: 1.500

  4 in total

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