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http://hdl.handle.net/20.500.12188/16829| DC Field | Value | Language |
|---|---|---|
| dc.contributor.author | Pejov, LJupcho | en_US |
| dc.contributor.author | Koteska, Bojana | en_US |
| dc.contributor.author | Mishev, Anastas | en_US |
| dc.date.accessioned | 2022-03-04T10:38:19Z | - |
| dc.date.available | 2022-03-04T10:38:19Z | - |
| dc.date.issued | 2020-12 | - |
| dc.identifier.uri | http://hdl.handle.net/20.500.12188/16829 | - |
| dc.description | Appropriate amount of initial nuclear kinetic energy corresponding to the desired temperature of the system (computed from statistical mechanics principles) was injected and distributed among the atoms. ADMP MD simulations were carried out in the NVE ensemble, avoiding application of any thermostats to keep the temperature constant throughout the simulations. Such approach was implemented since the main focus of the study is on computation of molecular vibrational dynamics at finite temperatures, within the time-correlation functions formalism. The files in the dataset contain the complete trajectories, i.e. both the initial equilibration phase of the MD simulations of 2 ps, which is subsequently followed by production phase of 11 ps. The Cholesky decomposition scheme has been used to obtain the orthonormal basis set. The time step that has been used to integrate the equations of motion was set to 0.1 fs. Electron fictious mass parameter was set to 0.1 atomic mass units (amu). The particular choices of the last two parameters were aimed to keep the adiabaticity index and the conditions for idempotency of the electronic density matrix within the literature recommended values throughout the whole trajectory. As mentioned, the MD trajectories in the dataset were generated by the semiempirical density functional tight binding method (DFTB). In the current study, the DFTBA implementation of this approach in the Gaussian09 system of codes has been used, which is based on analytical expressions for the matrix elements. | en_US |
| dc.description.abstract | The files in the dataset contain the complete trajectories from DFTB molecular dynamics (MD) simulations which were carried out by the atom-centered density matrix propagation scheme. Ten series of simulations were carried out, starting from the optimized geometries corresponding to the cis- and trans-conformers of formic acid. | en_US |
| dc.subject | Atom-centered density matrix propagation | en_US |
| dc.subject | Density Functional Tight Binding | en_US |
| dc.subject | Molecular dynamic | en_US |
| dc.subject | Finite-temperature vibrational dynamics | en_US |
| dc.subject | Formic acid | en_US |
| dc.title | Dataset for complete trajectories from ADMP DFTBA MD simulations of formic acid starting from the minima corresponding to cis and trans conformers at series of different temperatures | en_US |
| dc.type | Dataset | en_US |
| dc.relation.publication | Finite-Temperature Single Molecule Vibrational Dynamics from Combined Density Functional Tight Binding Extended Lagrangian Dynamics Simulations and Time Series Analysis | en_US |
| item.grantfulltext | open | - |
| item.fulltext | With Fulltext | - |
| crisitem.author.dept | Faculty of Computer Science and Engineering | - |
| crisitem.author.dept | Faculty of Computer Science and Engineering | - |
| crisitem.author.dept | Faculty of Natural Sciences and Mathematics | - |
| Appears in Collections: | UKIM 03: Datasets | |
Files in This Item:
| File | Опис | Size | Format | |
|---|---|---|---|---|
| fa-cis-dftba-admp-100k.out.zip | ADMP-DFTBA-FA-Cis conformation - temperature 100 K | 151.83 MB | Text | View/Open |
| fa-trans-dftba-admp-10k.out.zip | ADMP-DFTBA-FA-Trans conformation - temperature 10 K | 144.86 MB | Text | View/Open |
| fa-cis-dftba-admp-10k.out.zip | ADMP-DFTBA-FA-Cis conformation - temperature 10 K | 145.5 MB | Text | View/Open |
| fa-trans-dftba-admp-100k.out.zip | ADMP-DFTBA-FA-Trans conformation - temperature 100 K | 153.05 MB | Text | View/Open |
| fa-cis-dftba-admp-300k.out.zip | ADMP-DFTBA-FA-Cis conformation - temperature 300 K | 154.63 MB | Text | View/Open |
| fa-trans-dftba-admp-300k.out.zip | ADMP-DFTBA-FA-Trans conformation - temperature 300 K | 155.7 MB | Text | View/Open |
| fa-cis-dftba-admp-500k.out.zip | ADMP-DFTBA-FA-Cis conformation - temperature 500 K | 156.79 MB | Text | View/Open |
| fa-trans-dftba-admp-500k.out.zip | ADMP-DFTBA-FA-Trans conformation - temperature 500 K | 156.74 MB | Text | View/Open |
| fa-trans-dftba-admp-1000k.out.zip | ADMP-DFTBA-FA-Trans conformation - temperature 1000 K | 158.76 MB | Text | View/Open |
| fa-cis-dftba-admp-1000k.out.zip | ADMP-DFTBA-FA-Cis conformation - temperature 1000 K | 158.7 MB | Text | View/Open |
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