WebProp: Web interface for<i>ab initio</i>calculation of molecular one‐electron properties

Ganesh, V.; Kavathekar, Ritwik S.; Rahalkar, Anuja P.; Gadre, Shridhar R.

doi:10.1002/jcc.20802

Cited by 13 publications

(15 citation statements)

References 11 publications

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“…The opposite situation appears when fragments are treated completely independently [42, 43]. Intermediate situations are also possible [44–51]. However, one should remember that by simplifying the interactions and narrowing the variation space a systematic error is introduced.…”

Section: Introductionmentioning

confidence: 99%

Intermediate electrostatic field for the elongation method

Kuźniarowicz

Aoki

et al. 2014

J Mol Model

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A simple way to improve the accuracy of the fragmentation methods is proposed. The formalism was applied to the elongation (ELG) method at restricted open-shell Hartree-Fock (ROHF) level of theory. The α-helix conformer of polyglycine was taken as a model system. The modified ELG method includes a simplified electrostatic field resulting from point-charge distribution of the system’s environment. In this way the long-distance polarization is approximately taken into account. The field attenuates during the ELG process to eventually disappear when the final structure is reached. The point-charge distributions for each ELG step are obtained from charge sensitivity analysis (CSA) in force-field atoms resolution. The presence of the intermediate field improves the accuracy of ELG calculations. The errors in total energy and its kinetic and potential contributions are reduced by at least one-order of magnitude. In addition the SCF convergence of ROHF scheme is improved.

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Section: Introductionmentioning

confidence: 99%

Intermediate electrostatic field for the elongation method

Kuźniarowicz

Aoki

et al. 2014

J Mol Model

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“…In this Section, a few real usage scenarios for MeTA Studio APIs are presented. First, a description of how MeTA Studio APIs are used to build some parts of WebProp31 user interface is described. Later in the Section, examples of scripting MeTA Studio to build small and usable programs called “ChemLets” are described.…”

Section: Programming Meta Studio: Illustrative Examplesmentioning

confidence: 99%

“…WebProp,31 a web‐based system for evaluation of ab‐initio quality one‐electron properties was reported earlier by the author. One of the requirements while building the WebProp interface was to provide a user with an online viewer that also allows for interactive construction of a user defined grid on which to evaluate a particular scalar field (such as MESP or MED).…”

Section: Programming Meta Studio: Illustrative Examplesmentioning

confidence: 99%

MeTA studio: A cross platform, programmable IDE for computational chemist

Ganesh

2008

J Comput Chem

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Abstract:The development of a cross-platform, programmable integrated development environment (IDE), MeTA Studio, specifically tailored but not restricted to computational chemists working in the area of quantum chemistry with an emphasis on handling large molecules is presented. The IDE consists of a number of modules which include a visualizer and a programming and collaborative framework. The inbuilt viewer assists in visualizing molecules, their scalar fields, manually fragmenting a molecule, and introduces some innovative but simple techniques for handling large molecules. These include a simple Find language and simultaneous multiple camera views of the molecule. Basic tools needed to handle collaborative computing effectively are also included opening up new vistas for sharing ideas and information among computational chemists working on similar problems. MeTA Studio is an integrated programming environment that provides a rich set of application programming interfaces (APIs) which can be used to easily extend its functionality or build new applications as needed by the users.

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“…This especially involves analysis of MESP through its CPs and correlating the MESP values at the CPs with various chemical properties such as lone pair strength, site of electrophilic attack, etc. Previously, computer programs, such as WebProp and Fortran based rapid topography mapping code, have been designed by Gadre and coworkers for locating and characterizing the CPs of bare nuclear potential (BNP), MED, and MESP. UNIVIS‐2000 and MeTA studio are indigenously developed visualizers which aid the efficient visualization of these CPs along with isosurfaces, contours, etc.…”

Section: Introductionmentioning

confidence: 99%

DAMQT 2.1.0: A new version of the DAMQT package enabled with the topographical analysis of electron density and electrostatic potential in molecules

et al. 2015

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DAMQT-2.1.0 is a new version of DAMQT package which includes topographical analysis of molecular electron density (MED) and molecular electrostatic potential (MESP), such as mapping of critical points (CPs), creating molecular graphs, and atomic basins. Mapping of CPs is assisted with algorithmic determination of Euler characteristic in order to provide a necessary condition for locating all possible CPs. Apart from the mapping of CPs and determination of molecular graphs, the construction of MESP-based atomic basin is a new and exclusive feature introduced in DAMQT-2.1.0. The GUI in DAMQT provides a user-friendly interface to run the code and visualize the final outputs. MPI libraries have been implemented for all the tasks to develop the parallel version of the software. Almost linear scaling of computational time is achieved with the increasing number of processors while performing various aspects of topography. A brief discussion of molecular graph and atomic basin is provided in the current article highlighting their chemical importance. Appropriate example sets have been presented for demonstrating the functions and efficiency of the code.

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WebProp: Web interface forab initiocalculation of molecular one‐electron properties

Cited by 13 publications

References 11 publications

Intermediate electrostatic field for the elongation method

Intermediate electrostatic field for the elongation method

MeTA studio: A cross platform, programmable IDE for computational chemist

DAMQT 2.1.0: A new version of the DAMQT package enabled with the topographical analysis of electron density and electrostatic potential in molecules

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