scholarly journals Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes

2015 ◽  
Vol 143 (24) ◽  
pp. 243144 ◽  
Author(s):  
Christopher M. MacDermaid ◽  
Hemant K. Kashyap ◽  
Russell H. DeVane ◽  
Wataru Shinoda ◽  
Jeffery B. Klauda ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Cyclic Alkanes ◽  
Dynamics Simulations

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...

scholarly journals Refining amino acid hydrophobicity for dynamics simulation of membrane proteins

2017 ◽  
Author(s):  
Ronald D Hills, Jr
Keyword(s):  
Molecular Dynamics ◽  
Membrane Proteins ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Interfacial Behavior ◽  
Potentials Of Mean Force ◽  
Arginine Residues ◽  
Dynamics Simulations

Coarse-grained simulations enable the study of membrane proteins in the context of their native environment but require reliable parameters. The CgProt force field is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. The reassignment of polar sidechain sites was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues. The solvation energy at membrane depths of 0, 1.3 and 1.7 nm correlate with experimental partition coefficients in aqueous mixtures of cyclohexane, octanol and POPC, respectively, for sidechain analogs and Wimley-White peptides. These data points can be used to further discriminate between alternate force field parameters. Available partitioning data was also used to reparameterize the representation of the polar peptide backbone for non-alanine residues. The newly developed force field, CgProt 2.4, correctly predicts the global energy minimum in the potentials of mean force for insertion of the uncharged membrane-associated peptides LS3 and WALP23. CgProt will find application in molecular dynamics simulations of a variety of membrane protein systems.

scholarly journals Refining amino acid hydrophobicity for dynamics simulation of membrane proteins

2017 ◽  
Author(s):  
Ronald D Hills, Jr
Keyword(s):  
Molecular Dynamics ◽  
Membrane Proteins ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Interfacial Behavior ◽  
Potentials Of Mean Force ◽  
Arginine Residues ◽  
Dynamics Simulations

Coarse-grained simulations enable the study of membrane proteins in the context of their native environment but require reliable parameters. The CgProt force field is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. The reassignment of polar sidechain sites was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues. The solvation energy at membrane depths of 0, 1.3 and 1.7 nm correlate with experimental partition coefficients in aqueous mixtures of cyclohexane, octanol and POPC, respectively, for sidechain analogs and Wimley-White peptides. These data points can be used to further discriminate between alternate force field parameters. Available partitioning data was also used to reparameterize the representation of the polar peptide backbone for non-alanine residues. The newly developed force field, CgProt 2.4, correctly predicts the global energy minimum in the potentials of mean force for insertion of the uncharged membrane-associated peptides LS3 and WALP23. CgProt will find application in molecular dynamics simulations of a variety of membrane protein systems.

scholarly journals Coarse-grained force-field for large scale molecular dynamics simulations of polyacrylamide and polyacrylamide-gels based on quantum mechanics

2021 ◽  
Author(s):  
Mei Zheng ◽  
Andres Jaramillo-Botero ◽  
Xue-hai Ju ◽  
William A. Goddard
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Equation Of State ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Coarse Grained ◽  
Polyacrylamide Gels ◽  
Dynamics Simulations

Developing a coarse-grained force field for polyacrylamide based on quantum mechanics equation of state.

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>

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