Subject: Atom-centered density matrix propagation
Subject: Density Functional Tight Binding
Subject: Molecular dynamic
Subject: Finite-temperature vibrational dynamics
Subject: Formic acid
Year: 2020
Type: Dataset
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
Author: Pejov, LJupcho
Author: Koteska, Bojana
Author: Mishev, Anastas
Abstract: 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.
Publisher:
Relation: Finite-Temperature Single Molecule Vibrational Dynamics from Combined Density Functional Tight Binding Extended Lagrangian Dynamics Simulations and Time Series Analysis
Identifier: oai:repository.ukim.mk:20.500.12188/16829
Identifier: http://hdl.handle.net/20.500.12188/16829
