Steered Molecular Dynamics Studies of the Potential of Mean Force for Peptide Amphiphile Self-Assembly into Cylindrical Nanofibers

2013 ◽  
Vol 117 (32) ◽  
pp. 7453-7460 ◽  
Author(s):  
Tao Yu ◽  
One-Sun Lee ◽  
George C. Schatz
Keyword(s):  
Molecular Dynamics ◽  
Self Assembly ◽  
Steered Molecular Dynamics ◽  
Potential Of Mean Force ◽  
Peptide Amphiphile

scholarly journals Ranking protein-protein docking results using steered molecular dynamics and potential of mean force calculations

2016 ◽  
Vol 37 (20) ◽  
pp. 1861-1865 ◽  
Author(s):  
Laura J. Kingsley ◽  
Juan Esquivel-Rodríguez ◽  
Ying Yang ◽  
Daisuke Kihara ◽  
Markus A. Lill
Keyword(s):  
Molecular Dynamics ◽  
Steered Molecular Dynamics ◽  
Protein Docking ◽  
Potential Of Mean Force

Molecular dynamics simulations of self-assembled peptide amphiphile based cylindrical nanofibers

RSC Advances ◽  
2015 ◽  
Vol 5 (82) ◽  
pp. 66582-66590 ◽  
Author(s):  
E. Deniz Tekin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structural Properties ◽  
Self Assembly ◽  
The Self ◽  
Assembly Process ◽  
Peptide Amphiphile ◽  
Self Assembled ◽  
Dynamics Simulations

We carried out united-atom molecular dynamics simulations to understand the structural properties of peptide amphiphile (PA)-based cylindrical nanofibers and the factors that play a role in the “Self-Assembly” process on some specific nanofibers.

Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems

2019 ◽  
Author(s):  
Frédéric Célerse ◽  
Louis Lagardere ◽  
Étienne Derat ◽  
Jean-Philip Piquemal
Keyword(s):  
Molecular Dynamics ◽  
Parallel Implementation ◽  
Steered Molecular Dynamics ◽  
Massively Parallel

This paper is dedicated to the massively parallel implementation of Steered Molecular Dynamics in the Tinker-HP softwtare. It allows for direct comparisons of polarizable and non-polarizable simulations of realistic systems.

Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems

2019 ◽  
Author(s):  
Frédéric Célerse ◽  
Louis Lagardere ◽  
Étienne Derat ◽  
Jean-Philip Piquemal
Keyword(s):  
Molecular Dynamics ◽  
Parallel Implementation ◽  
Steered Molecular Dynamics ◽  
Massively Parallel

This paper is dedicated to the massively parallel implementation of Steered Molecular Dynamics in the Tinker-HP softwtare. It allows for direct comparisons of polarizable and non-polarizable simulations of realistic systems.

scholarly journals Sensitivity of Intra- and Intermolecular Interactions of Benzo[h]quinoline from Car–Parrinello Molecular Dynamics and Electronic Structure Inspection

2021 ◽  
Vol 22 (10) ◽  
pp. 5220
Author(s):  
Jarosław J. Panek ◽  
Joanna Zasada ◽  
Bartłomiej M. Szyja ◽  
Beata Kizior ◽  
Aneta Jezierska
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Quantum Effects ◽  
Potential Of Mean Force ◽  
Probability Density Distribution ◽  
Donor And Acceptor ◽  
Nuclear Quantum Effects ◽  
Vibrational Features

The O-H...N and O-H...O hydrogen bonds were investigated in 10-hydroxybenzo[h]quinoline (HBQ) and benzo[h]quinoline-2-methylresorcinol complex in vacuo, solvent and crystalline phases. The chosen systems contain analogous donor and acceptor moieties but differently coupled (intra- versus intermolecularly). Car–Parrinello molecular dynamics (CPMD) was employed to shed light onto principle components of interactions responsible for the self-assembly. It was applied to study the dynamics of the hydrogen bonds and vibrational features as well as to provide initial geometries for incorporation of quantum effects and electronic structure studies. The vibrational features were revealed using Fourier transformation of the autocorrelation function of atomic velocity and by inclusion of nuclear quantum effects on the O-H stretching solving vibrational Schrödinger equation a posteriori. The potential of mean force (Pmf) was computed for the whole trajectory to derive the probability density distribution and for the O-H stretching mode from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling and nuclear quantum effects. The electronic structure changes of the benzo[h]quinoline-2-methylresorcinol dimer and trimers were studied based on Constrained Density Functional Theory (CDFT) whereas the Electron Localization Function (ELF) method was applied for all systems. It was found that the bridged proton is localized on the donor side in both investigated systems in vacuo. The crystalline phase simulations indicated bridged proton-sharing and transfer events in HBQ. These effects are even more pronounced when nuclear quantization is taken into account, and the quantized Pmf allows the proton to sample the acceptor area more efficiently. The CDFT indicated the charge depletion at the bridged proton for the analyzed dimer and trimers in solvent. The ELF analysis showed the presence of the isolated proton (a signature of the strongest hydrogen bonds) only in some parts of the HBQ crystal simulation. The collected data underline the importance of the intramolecular coupling between the donor and acceptor moieties.

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