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).

A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions

2017 ◽  
Vol 146 (5) ◽  
pp. 054501 ◽  
Author(s):  
Julian Michalowsky ◽  
Lars V. Schäfer ◽  
Christian Holm ◽  
Jens Smiatek
Keyword(s):  
Force Field ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Coarse Grained ◽  
Water Model ◽  
Martini Force Field

The CHARMM36 Force Field for Lipids Can Be Used With More Accurate Water Models

2018 ◽  
Author(s):  
Fatima Sajadi ◽  
Christopher Rowley
Keyword(s):  
Dielectric Constant ◽  
Force Field ◽  
Lipid Bilayers ◽  
Form Factors ◽  
Water Model ◽  
Low Viscosity ◽  
Chemical Potentials ◽  
Water Models ◽  
Experimental Values ◽  
High Dielectric

The CHARMM36 force field for lipids is widely used in simulations of lipid bilayers. The CHARMM family of force fields were developed for use with the TIP3P water model. This water model has an anomalously high dielectric constant and low viscosity, which limits its accuracy in the calculation of quantities like permeability coefficients. The TIP3P-FB and TIP4P-FB water models are more accurate in terms of the dielectric constant and transport properties, which could allow more accurate simulations of systems containing water and lipids. To test whether the CHARMM36 lipid force field is compatible with the TIP3P-FB and TIP4P-FB water models, we have performed simulations of DPPC and POPC bilayers. The calculated headgroup area, compressibility, order parameters, and X-ray form factors are in good agreement with the experimental values, indicating that these improved water models can be used with the CHARMM36 lipid force field without modification. The water permeability predicted by these models is significantly different; the TIP3P-model diffusion in solution and at the lipid--water interface is anomalously fast due to the spuriously low viscosity of TIP3P-model water, but the PMF of permeation is higher for the TIP3P-FB and TIP4P-FB models due to their high excess chemical potentials.

scholarly journals A Reactive Force Field with Coarse-Grained Electrons for Liquid Water

2020 ◽  
Vol 11 (21) ◽  
pp. 9240-9247
Author(s):  
Itai Leven ◽  
Hongxia Hao ◽  
Akshaya Kumar Das ◽  
Teresa Head-Gordon
Keyword(s):  
Force Field ◽  
Liquid Water ◽  
Coarse Grained ◽  
Reactive Force ◽  
Reactive Force Field

Coarse graining of force fields for metal–organic frameworks

2016 ◽  
Vol 45 (10) ◽  
pp. 4370-4379 ◽  
Author(s):  
Johannes P. Dürholt ◽  
Raimondas Galvelis ◽  
Rochus Schmid
Keyword(s):  
Genetic Algorithm ◽  
Quantum Mechanic ◽  
Force Field ◽  
Reference Data ◽  
Metal Organic Frameworks ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Optimization Approach ◽  
Metal Organic ◽  
Force Field Parameters

We have adapted our genetic algorithm based optimization approach, originally developed to generate force field parameters from quantum mechanic reference data, to derive a first coarse grained force field for a MOF, taking the atomistic MOF-FF as a reference.

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.

scholarly journals Polarizable Water Model for the Coarse-Grained MARTINI Force Field

2010 ◽  
Vol 6 (6) ◽  
pp. e1000810 ◽  
Author(s):  
Semen O. Yesylevskyy ◽  
Lars V. Schäfer ◽  
Durba Sengupta ◽  
Siewert J. Marrink
Keyword(s):  
Force Field ◽  
Coarse Grained ◽  
Water Model ◽  
Martini Force Field

scholarly journals Coarse-Grained Simulation of Mechanical Properties of Single Microtubules With Micrometer Length

2021 ◽  
Vol 7 ◽  
Author(s):  
Jinyin Zha ◽  
Yuwei Zhang ◽  
Kelin Xia ◽  
Frauke Gräter ◽  
Fei Xia
Keyword(s):  
Electron Microscopy ◽  
Mechanical Properties ◽  
Coarse Graining ◽  
Vital Role ◽  
Large System ◽  
Coarse Grained ◽  
Biological Processes ◽  
Density Data ◽  
And Function ◽  
Microtubule Function

Microtubules are one of the most important components in the cytoskeleton and play a vital role in maintaining the shape and function of cells. Because single microtubules are some micrometers long, it is difficult to simulate such a large system using an all-atom model. In this work, we use the newly developed convolutional and K-means coarse-graining (CK-CG) method to establish an ultra-coarse-grained (UCG) model of a single microtubule, on the basis of the low electron microscopy density data of microtubules. We discuss the rationale of the micro-coarse-grained microtubule models of different resolutions and explore microtubule models up to 12-micron length. We use the devised microtubule model to quantify mechanical properties of microtubules of different lengths. Our model allows mesoscopic simulations of micrometer-level biomaterials and can be further used to study important biological processes related to microtubule function.

pSPICA: A Coarse-Grained Force Field for Lipid Membranes Based on a Polar Water Model

2019 ◽  
Vol 16 (1) ◽  
pp. 782-793 ◽  
Author(s):  
Yusuke Miyazaki ◽  
Susumu Okazaki ◽  
Wataru Shinoda
Keyword(s):  
Force Field ◽  
Lipid Membranes ◽  
Coarse Grained ◽  
Water Model ◽  
Polar Water
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