PSO-Assisted Development of New Transferable Coarse-Grained Water Models

2018 ◽  
Vol 122 (6) ◽  
pp. 1958-1971 ◽  
Author(s):  
Karteek K. Bejagam ◽  
Samrendra Singh ◽  
Yaxin An ◽  
Carter Berry ◽  
Sanket A. Deshmukh
Keyword(s):  
Coarse Grained ◽  
Water Models

Exploring the utility of coarse-grained water models for computational studies of interfacial systems

2010 ◽  
Vol 108 (15) ◽  
pp. 2007-2020 ◽  
Author(s):  
Xibing He ◽  
Wataru Shinoda ◽  
Russell DeVane ◽  
Michael L. Klein
Keyword(s):  
Coarse Grained ◽  
Computational Studies ◽  
Water Models

scholarly journals Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

2015 ◽  
Vol 142 (24) ◽  
pp. 244118 ◽  
Author(s):  
Julija Zavadlav ◽  
Manuel N. Melo ◽  
Siewert J. Marrink ◽  
Matej Praprotnik
Keyword(s):  
Coarse Grained ◽  
Adaptive Resolution ◽  
Water Models ◽  
Resolution Simulation

Development of Transferable Nonbonded Interactions between Coarse-Grained Hydrocarbon and Water Models

2019 ◽  
Vol 123 (4) ◽  
pp. 909-921 ◽  
Author(s):  
Yaxin An ◽  
Karteek K. Bejagam ◽  
Sanket A. Deshmukh
Keyword(s):  
Coarse Grained ◽  
Nonbonded Interactions ◽  
Water Models

Nanocomputation of Mechanical Properties in Nanobio Membrane

2011 ◽  
Vol 110-116 ◽  
pp. 3883-3887
Author(s):  
N. Maftouni ◽  
M. Amininassab ◽  
M. N. Mello ◽  
S. Marink
Keyword(s):  
Mechanical Properties ◽  
Pressure Profile ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Water Model ◽  
Near Surface ◽  
Martini Force Field ◽  
Water Region ◽  
Water Models ◽  
The Difference

It is very essential to know mechanical properties in different regions of nanobio membrane as one of the most important parts of living systems. Here the coarse-grained (CG) simulations method have been used to study the pressure profile in a system including nanobio membrane and water. CG simulations have become an important tool to study many biomolecular processes, exploring scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals particle. The effect of polarization has been ignored in the initial CG water molecules model. Given the important role of water as a solvent in biological systems, its treatment is very important to the properties derived from simulation studies. Till now two models have been parameterized to simulate water: i) standard MARTINI water and ii) polarizable coarse-grained water model. Both of mentioned water models are proper to be used in combination with the CG MARTINI force field. In this work both of these models have been used for simulation. One micro second CG molecular dynamics simulation has been done for two separate systems. Each system includes water and hydrated 1-palmitoyl-2-oleoyl-1-sn-3-phosphatidylcholine (POPC) lipid nanobio membrane. The difference between two systems is in simulated water models that one system has standard MARTINI water and the other one has polarizable water. In each case pressure profile calculation has been done via Virial pressure theorem. Results indicate that using polarizable water model leads to higher picks in pressure profile in water region near surface of nanobio membrane. This can be related to density of polarizable water and also may play role as a small barrier.

Multiscale Polarizable Coarse-graining Water Models on Cluster-level Electrostatic Dipoles

2021 ◽  
Author(s):  
Min Li ◽  
John Z.H. Zhang
Keyword(s):  
Force Field ◽  
Liquid Water ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Water Model ◽  
Biological Processes ◽  
Water Models ◽  
Cluster Level

The development of coarse-grained (CG) water model is increasingly important in CG studies of biological processes. In this work, we developed a generic CG force field of liquid water on...

Two-bead polarizable water models combined with a two-bead multipole force field (TMFF) for coarse-grained simulation of proteins

2017 ◽  
Vol 19 (10) ◽  
pp. 7410-7419 ◽  
Author(s):  
Min Li ◽  
John Z. H. Zhang
Keyword(s):  
Force Field ◽  
Coarse Grained ◽  
Water Model ◽  
Water Molecules ◽  
Water Models

(a) Four water molecules contained in the polarizable CG water models in (b) two-bead polarizable water model 1 (TPW1) and (c) two-bead polarizable water model 2 (TPW2).

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