Coarse-Grained Parameters for Divalent Cations within the SIRAH Force Field

2020 ◽  
Vol 60 (8) ◽  
pp. 3935-3943
Author(s):  
Florencia Klein ◽  
Daniela Cáceres ◽  
Mónica A. Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  
Keyword(s):  
Force Field ◽  
Divalent Cations ◽  
Coarse Grained

Parameterization of Divalent Cations for Coarse-Grained Simulations

2020 ◽  
Author(s):  
Florencia Klein ◽  
Daniela Cáceres-Rojas ◽  
Monica Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Divalent Cations ◽  
Computational Cost ◽  
Data Bank ◽  
Coarse Grained ◽  
Interaction Parameters ◽  
Dynamics Simulations ◽  
Dynamical Description

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>

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...

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

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

Fast Electrostatic Force and Moment Calculations in Multibody-Based Simulations of Coarse-Grained Biopolymers

2011 ◽  
Author(s):  
Mohammad Poursina ◽  
Jeremy Laflin ◽  
Kurt S. Anderson
Keyword(s):  
Force Field ◽  
Long Range ◽  
Electrostatic Force ◽  
Center Of Mass ◽  
Computational Cost ◽  
Field Approximation ◽  
The Body ◽  
Divide And Conquer ◽  
Coarse Grained ◽  
Coarse Grain

In molecular simulations, the dominant portion of the computational cost is associated with force field calculations. Herein, we extend the approach used to approximate long range gravitational force and the associated moment in spacecraft dynamics to the coulomb forces present in coarse grained biopolymer simulations. We approximate the resultant force and moment for long-range particle-body and body-body interactions due to the electrostatic force field. The resultant moment approximated here is due to the fact that the net force does not necessarily act through the center of mass of the body (pseudoatom). This moment is considered in multibody-based coarse grain simulations while neglected in bead models which use particle dynamics to address the dynamics of the system. A novel binary divide and conquer algorithm (BDCA) is presented to implement the force field approximation. The proposed algorithm is implemented by considering each rigid/flexible domain as a node of the leaf level of the binary tree. This substructuring strategy is well suited to coarse grain simulations of chain biopolymers using an articulated multibody approach.

scholarly journals SAFT-γ Force Field for the Simulation of Molecular Fluids. 5. Hetero-Group Coarse-Grained Models of Linear Alkanes and the Importance of Intramolecular Interactions

2018 ◽  
Vol 122 (39) ◽  
pp. 9161-9177 ◽  
Author(s):  
Sadia Rahman ◽  
Olga Lobanova ◽  
Guadalupe Jiménez-Serratos ◽  
Carlos Braga ◽  
Vasilios Raptis ◽  
...  
Keyword(s):  
Force Field ◽  
Intramolecular Interactions ◽  
Coarse Grained ◽  
Molecular Fluids ◽  
Linear Alkanes
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