Literature DB >> 22904601

Coarse-Grained Molecular Models of Water: A Review.

Kevin R Hadley1, Clare McCabe.   

Abstract

Coarse-grained (CG) models have proven to be very effective tools in the study of phenomena or systems that involve large time- and length-scales. By decreasing the degrees of freedom in the system and using softer interactions than seen in atomistic models, larger timesteps can be used and much longer simulation times can be studied. CG simulations are widely used to study systems of biological importance that are beyond the reach of atomistic simulation, necessitating a computationally efficient and accurate CG model for water. In this review, we discuss the methods used for developing CG water models and the relative advantages and disadvantages of the resulting models. In general, CG water models differ with regards to how many waters each CG group or bead represents, whether analytical or tabular potentials have been used to describe the interactions, and how the model incorporates electrostatic interactions. Finally, how the models are parameterized depends on their application, so, while some are fitted to experimental properties such as surface tension and density, others are fitted to radial distribution functions extracted from atomistic simulations.

Entities:  

Year:  2012        PMID: 22904601      PMCID: PMC3420348          DOI: 10.1080/08927022.2012.671942

Source DB:  PubMed          Journal:  Mol Simul        ISSN: 0892-7022            Impact factor:   2.178


  48 in total

1.  Structural transformation in supercooled water controls the crystallization rate of ice.

Authors:  Emily B Moore; Valeria Molinero
Journal:  Nature       Date:  2011-11-23       Impact factor: 49.962

2.  A new coarse-grained model for water: the importance of electrostatic interactions.

Authors:  Zhe Wu; Qiang Cui; Arun Yethiraj
Journal:  J Phys Chem B       Date:  2010-08-19       Impact factor: 2.991

3.  Transferability of Coarse Grained Potentials: Implicit Solvent Models for Hydrated Ions.

Authors:  Jia-Wei Shen; Chunli Li; Nico F A van der Vegt; Christine Peter
Journal:  J Chem Theory Comput       Date:  2011-05-05       Impact factor: 6.006

4.  On the investigation of coarse-grained models for water: balancing computational efficiency and the retention of structural properties.

Authors:  Kevin R Hadley; Clare McCabe
Journal:  J Phys Chem B       Date:  2010-04-08       Impact factor: 2.991

5.  A methane-water model for coarse-grained simulations of solutions and clathrate hydrates.

Authors:  Liam C Jacobson; Valeria Molinero
Journal:  J Phys Chem B       Date:  2010-06-03       Impact factor: 2.991

6.  A coarse-grained model of DNA with explicit solvation by water and ions.

Authors:  Robert C DeMille; Thomas E Cheatham; Valeria Molinero
Journal:  J Phys Chem B       Date:  2010-12-14       Impact factor: 2.991

7.  An automatic coarse-graining and fine-graining simulation method: application on polyethylene.

Authors:  Li-Jun Chen; Hu-Jun Qian; Zhong-Yuan Lu; Ze-Sheng Li; Chia-Chung Sun
Journal:  J Phys Chem B       Date:  2006-11-30       Impact factor: 2.991

8.  A Coarse-Grained Model Based on Morse Potential for Water and n-Alkanes.

Authors:  See-Wing Chiu; H Larry Scott; Eric Jakobsson
Journal:  J Chem Theory Comput       Date:  2010-02-17       Impact factor: 6.006

9.  Polarizable water model for the coarse-grained MARTINI force field.

Authors:  Semen O Yesylevskyy; Lars V Schäfer; Durba Sengupta; Siewert J Marrink
Journal:  PLoS Comput Biol       Date:  2010-06-10       Impact factor: 4.475

10.  Water Defect and Pore Formation in Atomistic and Coarse-Grained Lipid Membranes: Pushing the Limits of Coarse Graining.

Authors:  W F Drew Bennett; D Peter Tieleman
Journal:  J Chem Theory Comput       Date:  2011-08-17       Impact factor: 6.006

View more
  13 in total

1.  Coarse-grained molecular dynamics simulations of fibrin polymerization: effects of thrombin concentration on fibrin clot structure.

Authors:  Sumith Yesudasan; Xianqiao Wang; Rodney D Averett
Journal:  J Mol Model       Date:  2018-04-05       Impact factor: 1.810

Review 2.  From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field.

Authors:  Matías R Machado; Ari Zeida; Leonardo Darré; Sergio Pantano
Journal:  Interface Focus       Date:  2019-04-19       Impact factor: 3.906

3.  Assembly and Analysis of Cell-Scale Membrane Envelopes.

Authors:  Josh V Vermaas; Christopher G Mayne; Eric Shinn; Emad Tajkhorshid
Journal:  J Chem Inf Model       Date:  2021-12-15       Impact factor: 4.956

4.  Development of a coarse-grained water forcefield via multistate iterative Boltzmann inversion.

Authors:  Timothy C Moore; Christopher R Iacovella; Clare McCabe
Journal:  Found Mol Model Simul (2015)       Date:  2016-06-02

Review 5.  On the nature and use of models in network neuroscience.

Authors:  Danielle S Bassett; Perry Zurn; Joshua I Gold
Journal:  Nat Rev Neurosci       Date:  2018-09       Impact factor: 34.870

Review 6.  Water in Nanopores and Biological Channels: A Molecular Simulation Perspective.

Authors:  Charlotte I Lynch; Shanlin Rao; Mark S P Sansom
Journal:  Chem Rev       Date:  2020-08-25       Impact factor: 60.622

7.  Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA.

Authors:  S Y Mashayak; Mara N Jochum; Konstantin Koschke; N R Aluru; Victor Rühle; Christoph Junghans
Journal:  PLoS One       Date:  2015-07-20       Impact factor: 3.240

8.  Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

Authors:  Yuan Hu; Sudipta Kumar Sinha; Sandeep Patel
Journal:  J Phys Chem B       Date:  2014-10-07       Impact factor: 2.991

9.  The power of coarse graining in biomolecular simulations.

Authors:  Helgi I Ingólfsson; Cesar A Lopez; Jaakko J Uusitalo; Djurre H de Jong; Srinivasa M Gopal; Xavier Periole; Siewert J Marrink
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2014-05

10.  A Surface Site Interaction Point Method for Dissipative Particle Dynamics Parametrization: Application to Alkyl Ethoxylate Surfactant Self-Assembly.

Authors:  Ennio Lavagnini; Joanne L Cook; Patrick B Warren; Mark J Williamson; Christopher A Hunter
Journal:  J Phys Chem B       Date:  2020-06-08       Impact factor: 2.991

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.