Hybrid particle-field molecular dynamics simulations: Parallelization and benchmarks

2012 ◽  
Vol 33 (8) ◽  
pp. 868-880 ◽  
Author(s):  
Ying Zhao ◽  
Antonio De Nicola ◽  
Toshihiro Kawakatsu ◽  
Giuseppe Milano
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Particle Field ◽  
Hybrid Particle ◽  
Dynamics Simulations

scholarly journals Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in an Aqueous Environment

2018 ◽  
Vol 14 (9) ◽  
pp. 4928-4937 ◽  
Author(s):  
Hima Bindu Kolli ◽  
Antonio de Nicola ◽  
Sigbjørn Løland Bore ◽  
Ken Schäfer ◽  
Gregor Diezemann ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Aqueous Environment ◽  
Particle Field ◽  
Hybrid Particle ◽  
Dynamics Simulations

scholarly journals Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in Aqueous Environment

2018 ◽  
Author(s):  
Hima Bindu Kolli ◽  
Antonio de Nicola ◽  
Sigbjørn Løland Bore ◽  
Ken Schäfer ◽  
Gregor Diezemann ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Sodium Dodecyl ◽  
Intermolecular Forces ◽  
Coarse Grained ◽  
Qualitative Behavior ◽  
Aqueous Environment ◽  
Particle Field ◽  
Hybrid Particle ◽  
Dynamics Simulations

<p>We develop and test specific coarse-grained models for charged amphiphilic systems such as palmitoyloleoyl phosphatidylglycerol (POPG) lipid bilayer, and sodium dodecyl sulphate (SDS) surfactant in aqueous environment, to verify the ability of the hybrid particle-field method to provide a realistic description of polyelectrolyte soft-matter systems. The intramolecular interactions are treated by a standard molecular Hamiltonian and the non-electrostatic intermolecular forces are described by density fields. Electrostatics is introduced as an additional external field obtained by a modified particle-mesh Ewald procedure. Molecular dynamics simulations indicate that the methodology is robust with respect to the choice of the relative dielectric constant, yielding the same correct qualitative behavior for a broad range of dielectric values. In particular, our methodology reproduces well the organization of the POPG bilayer, as well as the SDS concentration-dependent change in the morphology of the micelles from spherical to microtubular aggregates. </p>

scholarly journals Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in Aqueous Environment

2018 ◽  
Author(s):  
Hima Bindu Kolli ◽  
Antonio de Nicola ◽  
Sigbjørn Løland Bore ◽  
Ken Schäfer ◽  
Gregor Diezemann ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Sodium Dodecyl ◽  
Intermolecular Forces ◽  
Coarse Grained ◽  
Qualitative Behavior ◽  
Aqueous Environment ◽  
Particle Field ◽  
Hybrid Particle ◽  
Dynamics Simulations

<p>We develop and test specific coarse-grained models for charged amphiphilic systems such as palmitoyloleoyl phosphatidylglycerol (POPG) lipid bilayer, and sodium dodecyl sulphate (SDS) surfactant in aqueous environment, to verify the ability of the hybrid particle-field method to provide a realistic description of polyelectrolyte soft-matter systems. The intramolecular interactions are treated by a standard molecular Hamiltonian and the non-electrostatic intermolecular forces are described by density fields. Electrostatics is introduced as an additional external field obtained by a modified particle-mesh Ewald procedure. Molecular dynamics simulations indicate that the methodology is robust with respect to the choice of the relative dielectric constant, yielding the same correct qualitative behavior for a broad range of dielectric values. In particular, our methodology reproduces well the organization of the POPG bilayer, as well as the SDS concentration-dependent change in the morphology of the micelles from spherical to microtubular aggregates. </p>

scholarly journals Molecular dynamics simulations in hybrid particle-continuum schemes: Pitfalls and caveats

2018 ◽  
Vol 224 ◽  
pp. 198-208 ◽  
Author(s):  
S. Stalter ◽  
L. Yelash ◽  
N. Emamy ◽  
A. Statt ◽  
M. Hanke ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Hybrid Particle ◽  
Dynamics Simulations
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