A COMPUTATIONAL GRID SYSTEM FOR QUANTUM CHEMICAL CALCULATIONS TESTED IN A MODELING OF THE GE(001) SURFACE

2005 ◽  
Vol 04 (01) ◽  
pp. 289-303 ◽  
Author(s):  
JAESIK KWAK ◽  
YOON SUP LEE

A computational Grid system with the simple architecture was constructed based on Globus and the concept of web application for the quantum chemical calculation. The computational Grid provides interfaces to a web-based input module and several molecular orbital calculation packages. Some aspects of the cluster modeling of the Ge (001) surface were tested on the constructed Grid. A number of conditions and parameters of the cluster model can be easily varied on the Grid, enabling concurrent testing of multiple choices of the model possible. These models were benchmarked on the Grid system. After that, the potential energy surface of the acetylene molecule moving over the model Ge (001) surface was scanned, in an effort to understand the adsorption reaction. Each point of the potential energy surface was calculated on the distributed node of the Grid system. These results demonstrate that the concept of high throughput computing can be successfully adapted to computational chemistry with a computational Grid. The result of modeling for the Ge surface itself is also described and could be of some interest.

2009 ◽  
Vol 113 (10) ◽  
pp. 1976-1984 ◽  
Author(s):  
Jiaxu Zhang ◽  
Upakarasamy Lourderaj ◽  
Srirangam V. Addepalli ◽  
Wibe A. de Jong ◽  
William L. Hase

2010 ◽  
Vol 63 (3) ◽  
pp. 379 ◽  
Author(s):  
Naomi L. Haworth ◽  
Jason Y. Liu ◽  
Samuel W. Fan ◽  
Jill E. Gready ◽  
Merridee A. Wouters

Disulfide torsional energy, a good predictor of disulfide redox potential in proteins, may be estimated by interpolation on a potential energy surface (PES) describing the twisting of diethyl disulfide through its three central dihedral angles. Here we update PES calculations at the M05-2X level of theory with the 6-31G(d) basis set. Although the surface shows no qualitative differences from an earlier MP2(full) PES, energy differences greater than 1 kJ mol–1 were seen for conformations with χ2 between –60° and 30°, or with χ3 below 60° or above 130°. This is particularly significant for highly strained disulfides that are likely to be spontaneously reduced by mechanical means. In benchmarking against the high-level G3X method, M05-2X showed significantly reduced root mean squared deviation compared with MP2(full) (1.0 versus 2.0 kJ mol–1 respectively). Results are incorporated into a web application that calculates relative torsional energies from disulfide dihedral angles (http://www.sbinf.org/applications/pes.html).


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