Please use this identifier to cite or link to this item: http://hdl.handle.net/20.500.12188/16829
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
Authors: Pejov, LJupcho 
Koteska, Bojana 
Mishev, Anastas 
Keywords: Atom-centered density matrix propagation
Density Functional Tight Binding
Molecular dynamic
Finite-temperature vibrational dynamics
Formic acid
Issue Date: Dec-2020
Related Publication: Finite-Temperature Single Molecule Vibrational Dynamics from Combined Density Functional Tight Binding Extended Lagrangian Dynamics Simulations and Time Series Analysis
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.
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.
URI: http://hdl.handle.net/20.500.12188/16829
Appears in Collections:UKIM 03: Datasets

Files in This Item:
File Description SizeFormat 
fa-cis-dftba-admp-100k.out.zipADMP-DFTBA-FA-Cis conformation - temperature 100 K151.83 MBTextView/Open
fa-trans-dftba-admp-10k.out.zipADMP-DFTBA-FA-Trans conformation - temperature 10 K144.86 MBTextView/Open
fa-cis-dftba-admp-10k.out.zipADMP-DFTBA-FA-Cis conformation - temperature 10 K145.5 MBTextView/Open
fa-trans-dftba-admp-100k.out.zipADMP-DFTBA-FA-Trans conformation - temperature 100 K153.05 MBTextView/Open
fa-cis-dftba-admp-300k.out.zipADMP-DFTBA-FA-Cis conformation - temperature 300 K154.63 MBTextView/Open
fa-trans-dftba-admp-300k.out.zipADMP-DFTBA-FA-Trans conformation - temperature 300 K155.7 MBTextView/Open
fa-cis-dftba-admp-500k.out.zipADMP-DFTBA-FA-Cis conformation - temperature 500 K156.79 MBTextView/Open
fa-trans-dftba-admp-500k.out.zipADMP-DFTBA-FA-Trans conformation - temperature 500 K156.74 MBTextView/Open
fa-trans-dftba-admp-1000k.out.zipADMP-DFTBA-FA-Trans conformation - temperature 1000 K158.76 MBTextView/Open
fa-cis-dftba-admp-1000k.out.zipADMP-DFTBA-FA-Cis conformation - temperature 1000 K158.7 MBTextView/Open
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