NEXMD Software Package for Nonadiabatic Excited State Molecular Dynamics Simulations

2020 ◽  
Vol 16 (9) ◽  
pp. 5771-5783 ◽  
Author(s):  
Walter Malone ◽  
Benjamin Nebgen ◽  
Alexander White ◽  
Yu Zhang ◽  
Huajing Song ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Molecular Dynamics Simulations ◽  
Software Package ◽  
Dynamics Simulations

Mechanistic analysis of light-driven overcrowded alkene-based molecular motors by multiscale molecular simulations

2021 ◽  
Vol 23 (14) ◽  
pp. 8525-8540
Author(s):  
Mudong Feng ◽  
Michael K. Gilson
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Molecular Dynamics Simulations ◽  
Ground State ◽  
Molecular Motors ◽  
Motor Performance ◽  
Molecular Simulations ◽  
Mechanistic Analysis ◽  
Dynamics Simulations ◽  
Shed Light

Ground-state and excited-state molecular dynamics simulations shed light on the rotation mechanism of small, light-driven molecular motors and predict motor performance. How fast can they rotate; how much torque and power can they generate?

Ab Initio Molecular Dynamics Simulations of an Excited State of X-(H2O)3(X = Cl, I) Complex

2005 ◽  
Vol 109 (42) ◽  
pp. 9419-9423 ◽  
Author(s):  
M. Kołaski ◽  
Han Myoung Lee ◽  
Chaeho Pak ◽  
M. Dupuis ◽  
Kwang S. Kim
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Dynamics Simulations

Photorelaxation of imidazole and adenine via electron-driven proton transfer along H2O wires

2016 ◽  
Vol 195 ◽  
pp. 237-251 ◽  
Author(s):  
Rafał Szabla ◽  
Robert W. Góra ◽  
Mikołaj Janicki ◽  
Jiří Šponer
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Potential Energy ◽  
Proton Transfer ◽  
Potential Energy Surface ◽  
Molecular Dynamics Simulations ◽  
Gas Phase ◽  
Energy Surface ◽  
Water Molecules ◽  
Dynamics Simulations

Photochemically created πσ* states were classified among the most prominent factors determining the ultrafast radiationless deactivation and photostability of many biomolecular building blocks. In the past two decades, the gas phase photochemistry of πσ* excitations was extensively investigated and was attributed to N–H and O–H bond fission processes. However, complete understanding of the complex photorelaxation pathways of πσ* states in the aqueous environment was very challenging, owing to the direct participation of solvent molecules in the excited-state deactivation. Here, we present non-adiabatic molecular dynamics simulations and potential energy surface calculations of the photoexcited imidazole–(H2O)5 cluster using the algebraic diagrammatic construction method to the second-order [ADC(2)]. We show that electron driven proton transfer (EDPT) along a wire of at least two water molecules may lead to the formation of a πσ*/S0 state crossing, similarly to what we suggested for 2-aminooxazole. We expand on our previous findings by direct comparison of the imidazole–(H2O)5 cluster to non-adiabatic molecular dynamics simulations of imidazole in the gas phase, which reveal that the presence of water molecules extends the overall excited-state lifetime of the chromophore. To embed the results in a biological context, we provide calculations of potential energy surface cuts for the analogous photorelaxation mechanism present in adenine, which contains an imidazole ring in its structure.

scholarly journals Sharing Data from Molecular Simulations

2019 ◽  
Author(s):  
Mark J. Abraham ◽  
Rossen Apostolov ◽  
Jonathan Barnoud ◽  
Paul Bauer ◽  
Christian Blau ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Best Practices ◽  
Molecular Dynamics Simulations ◽  
Software Package ◽  
Molecular Simulations ◽  
Md Simulations ◽  
Scientific Output ◽  
Level Of Detail ◽  
Simulation Data ◽  
Dynamics Simulations

Given the need for modern researchers to produce open, reproducible scientific output, the lack of standards and best practices for sharing data and workflows used to produce and analyze molecular dynamics (MD) simulations have become an important issue in the field. There are now multiple well-established packages to perform molecular dynamics simulations, often highly tuned for exploiting specific classes of hardware, and each with strong communities surrounding them, but with very limited interoperability/transferability options. Thus, the choice of the software package often dictates the workflow for both simulation production and analysis. The level of detail in documenting the workflows and analysis code varies greatly in published work, hindering reproducibility of the reported results and the ability for other researchers to build on these studies. An increasing number of researchers are motivated to make their data available, but many challenges remain in order to effectively share and reuse simulation data. To discuss these and other issues related to best practices in the field in general, we organized a workshop in November 2018 ( <a href="https://bioexcel.eu/events/workshop-on-sharing-data-from-molecular-simulations/">https://bioexcel.eu/events/workshop-on-sharing-data-from-molecular-simulations/</a>). Here, we present a brief overview of this workshop and topics discussed. We hope this effort will spark further conversation in the MD community to pave the way towards more open, interoperable and reproducible outputs coming from research studies using MD simulations.

scholarly journals Sharing Data from Molecular Simulations

2019 ◽  
Author(s):  
Mark J. Abraham ◽  
Rossen Apostolov ◽  
Jonathan Barnoud ◽  
Paul Bauer ◽  
Christian Blau ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Best Practices ◽  
Molecular Dynamics Simulations ◽  
Software Package ◽  
Molecular Simulations ◽  
Md Simulations ◽  
Scientific Output ◽  
Level Of Detail ◽  
Simulation Data ◽  
Dynamics Simulations

Given the need for modern researchers to produce open, reproducible scientific output, the lack of standards and best practices for sharing data and workflows used to produce and analyze molecular dynamics (MD) simulations have become an important issue in the field. There are now multiple well-established packages to perform molecular dynamics simulations, often highly tuned for exploiting specific classes of hardware, and each with strong communities surrounding them, but with very limited interoperability/transferability options. Thus, the choice of the software package often dictates the workflow for both simulation production and analysis. The level of detail in documenting the workflows and analysis code varies greatly in published work, hindering reproducibility of the reported results and the ability for other researchers to build on these studies. An increasing number of researchers are motivated to make their data available, but many challenges remain in order to effectively share and reuse simulation data. To discuss these and other issues related to best practices in the field in general, we organized a workshop in November 2018 ( <a href="https://bioexcel.eu/events/workshop-on-sharing-data-from-molecular-simulations/">https://bioexcel.eu/events/workshop-on-sharing-data-from-molecular-simulations/</a>). Here, we present a brief overview of this workshop and topics discussed. We hope this effort will spark further conversation in the MD community to pave the way towards more open, interoperable and reproducible outputs coming from research studies using MD simulations.

scholarly journals Dynamics of the excited-state hydrogen transfer in a (dG)·(dC) homopolymer: intrinsic photostability of DNA

2018 ◽  
Vol 9 (41) ◽  
pp. 7902-7911 ◽  
Author(s):  
Antonio Francés-Monerris ◽  
Hugo Gattuso ◽  
Daniel Roca-Sanjuán ◽  
Iñaki Tuñón ◽  
Marco Marazzi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Molecular Dynamics Simulations ◽  
Hydrogen Transfer ◽  
Proton Transfers ◽  
Out Of Plane ◽  
Dynamics Simulations

Multiscale molecular dynamics simulations reveal out-of-plane distortions that favour DNA photostability. A novel photostability mechanism involving four proton transfers and triggered by a nearby Na+ ion is also unveiled.

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