Workflows
http://hdl.handle.net/21.15102/VISEEM-270
This sub-section contains workflows of the VI-SEEM Life Sciences community2021-01-20T15:28:11ZDataset from the study “SEMIEMPIRICAL ATOM-CENTERED DENSITY MATRIX PROPAGATION APPROACH TO TEMPERATURE-DEPENDENT VIBRATIONAL SPECTROSCOPY OF IRINOTECAN”
http://hdl.handle.net/21.15102/VISEEM-348
Dataset from the study “SEMIEMPIRICAL ATOM-CENTERED DENSITY MATRIX PROPAGATION APPROACH TO TEMPERATURE-DEPENDENT VIBRATIONAL SPECTROSCOPY OF IRINOTECAN”
Pejov, Ljupco
This dataset contains the complete molecular dynamics (MD) trajectories of free irinotecan molecule at several temperatures. MD study of irinotecan molecule was carried out with the atom-centered density matrix propagation scheme at AM1 semiempirical level of theory, at series of different temperatures, ranging from 5 K to 300 K. Molecular dynamics simulations were performed within the NVE ensemble, initially injecting (and redistributing among the nuclei) various amounts of nuclear kinetic energies to achieve the desired target temperatures. Subsequently to initial equilibration phase of 2 ps, productive simulations were carried out for 8 ps. The accuracy of simulations and the closeness of the generated trajectory to those at the Born-Oppenheimer surface were carefully followed and analyzed. To compute the temperature-dependent rovibrational density of states spectra, the velocity-velocity autocorrelation functions were computed and Fourier-transformed. Fourier-transformed dipole moment autocorrelation functions were, on the other hand, used to calculate the temperature-dependent infrared absorption cross section spectra. The finite-temperature spectra were compared to those computed by a static approach, i.e. by diagonalization of mass-weighted Hessian matrices at the minima located on the potential energy surfaces. Thermally-induced spectral changes were analyzed and discussed. The advantages of finite-temperature statistical physics simulations based on semiempirical Hamiltonian over the static semiempirical ones in the case of complex, physiologically active molecular systems relevant to intermolecular interactions between drugs and drug carriers were pointed out and discussed.
The complete ADMP trajectories, including both equilibration and production phases, together with the extracted time series of nuclear kinetic energies, total dipole moment and its components, integrand for subsequent velocity-velocity autocorrelation function as well as the adiabaticity index.
2018-05-17T00:00:00ZCalculation of Local Mode Frequencies (Partial Vibrational Density of States) from Classical or AB Initio Molecular Dynamics Simulations
http://hdl.handle.net/21.15102/VISEEM-271
Calculation of Local Mode Frequencies (Partial Vibrational Density of States) from Classical or AB Initio Molecular Dynamics Simulations
Pejov, Ljupco
Development of analytic derivatives techniques in computational quantum chemistry has paved the way towards practically routine algorithms for computation of vibrational spectroscopic properties of even large molecular systems. In popular quantum chemistry codes, algorithms have been encoded that allow practically “black-box” sequential optimization of molecular geometries (in the sense of locating stationary points on potential energy hypersurfaces in Born-Oppenheimer sense) and harmonic vibrational analyses, performed by diagonalization of mass-weighted Hessian matrices. Aside from harmonic vibrational spectra, harmonic vibrational analyses enable a check of the character of the located stationary point on the molecular PES (minimum vs. saddle point of some order). However, the calculations of the previously mentioned type effectively treat isolated molecular species in vacuum, at T = 0 K. Much more often, in realistic applications, one is interested in molecular species embedded in some medium (solvent, solid matrix etc.) at finite temperature, usually much above absolute zero. To account for the variety of different thermally-induced configurations of a molecular system embedded e.g. in a liquid solvent, statistical physics simulations need to be performed (such as, e.g. Monte Carlo – MC or molecular dynamics – MD). In this scientific workflow, we will focus on a method for efficient processing of the results from MD simulations.
In this scientific workflow a method for efficient processing of the results from MD simulations is presented. In the particular case considered, the results from Born-Oppenheimer MD (BOMD) simulations, generated either with Gaussian09 or ORCA 4.0 series of codes will be used.
2017-01-01T00:00:00Z