scholarly journals Task-based Parallel Computation of the Density Matrix in Quantum-based Molecular Dynamics using Graph Partitioning

2017 ◽  
Vol 39 (6) ◽  
pp. C466-C480 ◽  
Author(s):  
Purnima Ghale ◽  
Matthew P. Kroonblawd ◽  
Sue Mniszewski ◽  
Christian F. A. Negre ◽  
Robert Pavel ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Matrix ◽  
Parallel Computation ◽  
Graph Partitioning

Ab initio molecular dynamics: Propagating the density matrix with gaussian orbitals. IV. Formal analysis of the deviations from born-oppenheimer dynamics

2002 ◽  
Vol 42 (2-3) ◽  
pp. 191-202 ◽  
Author(s):  
Srinivasan S. Iyengar ◽  
H. Bernhard Schlegel ◽  
Gregory A. Voth ◽  
John M. Millam ◽  
Gustavo E. Scuseria ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Matrix ◽  
Ab Initio ◽  
Formal Analysis ◽  
Ab Initio Molecular Dynamics ◽  
Gaussian Orbitals

scholarly journals Semiempirical Atom-centered Density Matrix Propagation Approach to Temperature-dependent Vibrational Spectroscopy of Irinotecan

2018 ◽  
Vol 19 (2) ◽  
pp. 149-159
Author(s):  
Bojana Koteska ◽  
Maja Simonoska Crcarevska ◽  
Marija Glavas Dodov ◽  
Jasmina Tonic Ribarska ◽  
Ljupco Pejov
Keyword(s):  
Molecular Dynamics ◽  
Density Matrix ◽  
Finite Temperature ◽  
Potential Energy Surfaces ◽  
Statistical Physics ◽  
Drug Carriers ◽  
Temperature Dependent ◽  
Autocorrelation Functions ◽  
Thermally Induced ◽  
Dynamics Simulations

In the present study, a molecular dynamics study of irinotecan molecule with the atom-centered density matrix propagation scheme was carried out 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.

scholarly journals Graph Partitioning Methods for Fast Parallel Quantum Molecular Dynamics

2016 ◽  
pp. 42-51 ◽  
Author(s):  
Hristo N. Djidjev ◽  
Georg Hahn ◽  
Susan M. Mniszewski ◽  
Christian F.A. Negre ◽  
Anders M.N. Niklasson ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Graph Partitioning ◽  
Quantum Molecular Dynamics ◽  
Partitioning Methods

scholarly journals Theoretical insights into the dissociation process for dissociative electron attachment to adenine and its tautomer

2020 ◽  
Vol 38 (4) ◽  
pp. 277-284
Author(s):  
Ying Zhang ◽  
Xing Wang ◽  
Zhongfeng Xu
Keyword(s):  
Molecular Dynamics ◽  
Density Matrix ◽  
Gas Phase ◽  
Electron Attachment ◽  
Closed Shell ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Dissociative Electron Attachment ◽  
Dissociation Process ◽  
First Time

AbstractThe ab initio molecular dynamics (MD) simulations using an atom-centered density matrix propagation method are carried out in the first time to investigate the dissociative electron attachment (DEA) processes of adenine and its tautomer in the gas phase. Since the incoming electron are captured on the lowest π∗ anti-bond orbital, which is led to the different N–H bond, the C–H bond and the C–N bond are broken. The dominant anion observed in DEA dissociation process is the closed-shell dehydrogenated anion (Ade − H)−. The additional anions (Ade − NH2)− and (Ade − 2H)− are also obtained in ADMP simulation. The results are well consistent with the previous DEA experimental results. Thus, the ADMP method is used to gain a more intuitive and better understanding of the necessary dissociation process in the DEA experiment.

scholarly journals Graph Partitioning Methods for Fast Parallel Quantum Molecular Dynamics

2016 ◽  
Author(s):  
Hristo Nikolov Djidjev ◽  
Georg Hahn ◽  
Susan M. Mniszewski ◽  
Christian Francisco Negre ◽  
Anders Mauritz Niklasson ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Graph Partitioning ◽  
Quantum Molecular Dynamics ◽  
Partitioning Methods
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