Literature DB >> 17430062

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

Matej Praprotnik1, Luigi Delle Site, Kurt Kremer.   

Abstract

The authors report adaptive resolution molecular dynamics simulations of a flexible linear polymer in solution. The solvent, i.e., a liquid of tetrahedral molecules, is represented within a certain radius from the polymer's center of mass with a high level of detail, while a lower coarse-grained resolution is used for the more distant solvent. The high resolution sphere moves with the polymer and freely exchanges molecules with the low resolution region through a transition regime. The solvent molecules change their resolution and number of degrees of freedom on the fly. The authors show that their approach correctly reproduces the static and dynamic properties of the polymer chain and surrounding solvent.

Entities:  

Mesh:

Substances:

Year:  2007        PMID: 17430062     DOI: 10.1063/1.2714540

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  6 in total

1.  Reference state for the generalized Yvon-Born-Green theory: application for coarse-grained model of hydrophobic hydration.

Authors:  J W Mullinax; W G Noid
Journal:  J Chem Phys       Date:  2010-09-28       Impact factor: 3.488

2.  The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models.

Authors:  W G Noid; Pu Liu; Yanting Wang; Jhih-Wei Chu; Gary S Ayton; Sergei Izvekov; Hans C Andersen; Gregory A Voth
Journal:  J Chem Phys       Date:  2008-06-28       Impact factor: 3.488

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

Authors:  Maziar Heidari; Robinson Cortes-Huerto; Kurt Kremer; Raffaello Potestio
Journal:  Eur Phys J E Soft Matter       Date:  2018-05-23       Impact factor: 1.890

4.  Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units.

Authors:  Artem B Mamonov; Steven Lettieri; Ying Ding; Jessica L Sarver; Rohith Palli; Timothy F Cunningham; Sunil Saxena; Daniel M Zuckerman
Journal:  J Chem Theory Comput       Date:  2012-06-15       Impact factor: 6.006

5.  The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models.

Authors:  W G Noid; Jhih-Wei Chu; Gary S Ayton; Vinod Krishna; Sergei Izvekov; Gregory A Voth; Avisek Das; Hans C Andersen
Journal:  J Chem Phys       Date:  2008-06-28       Impact factor: 3.488

6.  Ligand-protein interactions in lysozyme investigated through a dual-resolution model.

Authors:  Raffaele Fiorentini; Kurt Kremer; Raffaello Potestio
Journal:  Proteins       Date:  2020-06-15
  6 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.