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

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

scholarly journals The SPICA Coarse-Grained Force Field for Proteins and Peptides

2021 ◽  
Author(s):  
Shuhei Kawamoto ◽  
Huihui Liu ◽  
Sangjae Seo ◽  
Yusuke Miyazaki ◽  
Mayank Dixit ◽  
...  
Keyword(s):  
Force Field ◽  
Lipid Membranes ◽  
Lipid Membrane ◽  
Coarse Grained ◽  
Transmembrane Helices ◽  
Free Energies ◽  
Transmembrane Peptides ◽  
Energy Profiles ◽  
Protein Model ◽  
Preliminary Version

ABSTRACTA coarse-grained (CG) model for peptides and proteins was developed as an extension of the SPICA (Surface Property fItting Coarse grAined) force field (FF). The model was designed to examine membrane proteins that are fully compatible with the lipid membranes of the SPICA FF. A preliminary version of this protein model was created using thermodynamic properties, including the surface tension and density in the SPICA (formerly called SDK) FF. In this study, we improved the CG protein model to facilitate molecular dynamics (MD) simulation with a reproduction of multiple properties from both experiments and all-atom (AA) simulations. The side chain analogs reproduced the transfer free energy profiles across the lipid membrane and demonstrated reasonable dimerization free energies in water compared to those from AA-MD. A series of peptides/proteins adsorbed or penetrated into the membrane simulated by the CG-MD correctly predicted the penetration depths and tilt angles of peripheral and transmembrane peptides/proteins comparable to those in the orientation of protein in membrane (OPM) database. In addition, the dimerization free energies of several transmembrane helices within a lipid bilayer were comparable to those from experimental estimation. Application studies on a series of membrane protein assemblies, scramblases, and poliovirus capsids demonstrated a good performance of the SPICA FF.

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

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).

scholarly journals Martini Coarse-Grained Force Field: Extension to RNA

2017 ◽  
Vol 113 (2) ◽  
pp. 246-256 ◽  
Author(s):  
Jaakko J. Uusitalo ◽  
Helgi I. Ingólfsson ◽  
Siewert J. Marrink ◽  
Ignacio Faustino
Keyword(s):  
Force Field ◽  
Field Extension ◽  
Coarse Grained
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