Protein simulation using coarse-grained two-bead multipole force field with polarizable water models

2017 ◽  
Vol 146 (6) ◽  
pp. 065101
Author(s):  
Min Li ◽  
John Z. H. Zhang
Keyword(s):  
Force Field ◽  
Coarse Grained ◽  
Protein Simulation ◽  
Water Models

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

scholarly journals A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields

2018 ◽  
Vol 39 (28) ◽  
pp. 2360-2370 ◽  
Author(s):  
Adam K. Sieradzan ◽  
Artur Giełdoń ◽  
Yanping Yin ◽  
Yi He ◽  
Harold A. Scheraga ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Force Field ◽  
Force Fields ◽  
Coarse Grained ◽  
Protein Nucleic Acid ◽  
New Protein

scholarly journals A Generic Force Field for Simulating Native Protein Structures Using Dissipative Particle Dynamics

Soft Matter ◽  
2021 ◽  
Author(s):  
Rakesh K Vaiwala ◽  
Ganapathy Ayappa
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dissipative Particle Dynamics ◽  
Protein Structures ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Native Protein ◽  
Dynamics Simulations

A coarse-grained force field for molecular dynamics simulations of native structures of proteins in a dissipative particle dynamics (DPD) framework is developed. The parameters for bonded interactions are derived by...

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

Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer

2019 ◽  
Vol 123 (37) ◽  
pp. 7829-7839
Author(s):  
Karolina Ziȩba ◽  
Magdalena Ślusarz ◽  
Rafał Ślusarz ◽  
Adam Liwo ◽  
Cezary Czaplewski ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Force Field ◽  
Lipid Bilayer ◽  
Coarse Grained
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