Topics

Car-Parrinello Monitor for more robust Born-Oppenheimer molecular dynamics.

08:00 EDT 18th July 2019 | BioPortfolio

Summary of "Car-Parrinello Monitor for more robust Born-Oppenheimer molecular dynamics."

Born-Oppenheimer molecular dynamics (BOMD) is a promising simulation method for exploring the possible reaction pathways of a chemical system, but one significant challenge is the increased difficulty of converging the self-consistent field (SCF) calculation that often accompanies the breaking and forming of chemical bonds. To address this challenge, we developed an enhancement to the BOMD simulation method called the Car-Parrinello monitor (CPMonitor) that uses Car-Parrinello molecular dynamics (CPMD) to recover from SCF convergence failures. CPMonitor works by detecting SCF convergence failures in BOMD and switching to a CPMD Hamiltonian to propagate through the region of configuration space where the SCF calculation is unable to converge, then switching back to BOMD when good convergence behavior is re-established. We present a series of simulation studies that use CPMonitor, including detailed studies of the thermodynamic and dynamical properties of simple systems, as well as nanoreactor simulations containing transition metal atoms that were previously not possible to simulate using standard BOMD methods. Our studies show that CPMonitor can make BOMD simulations robust to SCF convergence difficulties and improve simulation performance and stability in reaction discovery applications.

Affiliation

Journal Details

This article was published in the following journal.

Name: Journal of chemical theory and computation
ISSN: 1549-9626
Pages:

Links

DeepDyve research library

PubMed Articles [14999 Associated PubMed Articles listed on BioPortfolio]

On the calculation of quantum mechanical electron transfer rates.

We present a simple interpolation formula for the rate of an electron transfer reaction as a function of the electronic coupling strength. The formula only requires the calculation of Fermi golden rul...

Shannon Entropy and Fisher information from a Non-Born Oppenheimer Perspective.

We study the Shannon entropy and the Fisher information in a non-Born- Oppenheimer (nBO) regime, where these quantities are constructed from one-particle densities obtained from an exact nBO analytic ...

Charge-tagged DNA Radicals in the Gas Phase Characterized by UV-Vis Photodissociation Action Spectroscopy.

Adenosine radicals tagged with a fixed-charge group were generated in the gas phase and structurally characterized by tandem mass spectrometry, deuterium labeling and UV-Vis action spectroscopy. Exper...

Metadynamics for automatic sampling of quantum property manifolds: exploration of molecular biradicality landscapes.

We present a general extension of the metadynamics allowing for an automatic sampling of quantum property manifolds (ASQPM) giving rise to functional landscapes that are analogous to the potential ene...

Non-adiabatic Excited-State Molecular Dynamics: Theory and Applications for Modeling Photophysics in Extended Molecular Materials.

Optically active molecular materials, such as organic conjugated polymers and biological systems, are characterized by strong coupling between electronic and vibrational degrees of freedom. Typically,...

Clinical Trials [4797 Associated Clinical Trials listed on BioPortfolio]

Chemotherapy, Host Response and Molecular Dynamics in Periampullary Cancer

The CHAMP (Chemotherapy, Host response And Molecular dynamics in Periampullary cancer) study is a prospective, single-arm observational study that started Sept 1 2018. Patients diagnosed w...

Evaluation of Use of Brain Activity Monitoring Dynamics in ADHD

This study evaluates the ability to support diagnosis and monitor of the dynamics in ADD/ADHD subjects with an easy to use EEG Device.

A Multi-National Study In Bladder Cancer Patients to Detect Recurrences After TURB (Trans-urethral Resection of the Bladder) Earlier With the Xpert Bladder Cancer Monitor Assay (ANTICIPATE X)

Bladder cancer is the 5th most common cancer in Europe, with more than 151,000 new cases diagnosed in 2012 (4% of the total). Bladder cancer has the highest recurrence rate of any malignan...

Lung Obstruction in Adulthood of Prematurely Born (LUNAPRE)

Obstructive lung disease is an increasing global health problem of pandemic proportions, with COPD alone affecting >10% of the population. Smoking is the main and most well studies risk fa...

HIV-DNA Dynamics in HIV Monoinfected or HIV/HCV Coinfected Patients

New markers of viral activity are now under investigation. Aim of the study is to investigate the efficacy of new antiretroviral drugs by monitoring HIV-DNA dynamics in HIV-positive popula...

Medical and Biotech [MESH] Definitions

A computer simulation developed to study the motion of molecules over a period of time.

A spectroscopic technique which uses the Mossbauer effect (inelastic scattering of gamma radiation resulting from interaction with heavy nuclei) to monitor the small variations in the interaction between an atomic nucleus and its environment. Such variations may be induced by changes in temperature, pressure, chemical state, molecular conformation, molecular interaction, or physical site. It is particularly useful for studies of structure-activity relationship in metalloproteins, mobility of heavy metals, and the state of whole tissue and cell membranes.

The use of molecularly targeted imaging probes to localize and/or monitor biochemical and cellular processes via various imaging modalities that include RADIONUCLIDE IMAGING; ULTRASONOGRAPHY; MAGNETIC RESONANCE IMAGING; fluorescence imaging; and MICROSCOPY.

Non-invasive imaging of cells that have been labeled non-destructively, such as with nanoemulsions or reporter genes that can be detected by molecular imaging, to monitor their location, viability, cell lineage expansion, response to drugs, movement, or other behaviors in vivo.

Large, robust forms of brown algae (PHAEOPHYCEAE) in the order Laminariales. They are a major component of the lower intertidal and sublittoral zones on rocky coasts in temperate and polar waters. Kelp, a kind of SEAWEED, usually refers to species in the genera LAMINARIA or MACROCYSTIS, but the term may also be used for species in FUCUS or Nereocystis.

Quick Search


DeepDyve research library

Searches Linking to this Article