Abstract
InSilicoLab for Chemistry with its experiments and QC Advisor are the tools assisting PL-Grid users in chemistry computations on grid infrastructure. The tools are designed to help the user at all stages of calculations – from the software choice and input data preparation, through job submission and monitoring to the retrieval of output files and analysis of results. General Quantum Chemistry experiment helps in launching QC computations on PL-Grid. A specialized tool – Trajectory Sculptor – is designed for manipulations with Molecular Dynamics trajectories and large sets of molecular structures in sequential computational experiments. QC Advisor collects information about availability of different computational methods in quantum-chemical programs and supports preparation of input files for the most popular software. The main idea behind the tools described in the paper is to reduce the effort needed to set-up the calculations, allowing users to focus on scientific content of their work.
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References
The 2013 Nobel Prize in Chemistry – Laureates (2013), http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2013/
Computational Chemistry List, http://www.ccl.net/
Bosak, B., Komasa, J., Kopta, P., Kurowski, K., Mamoński, M., Piontek, T.: New Capabilities in QosCosGrid Middleware for Advanced Job Management, Advance Reservation and Co-allocation of Computing Resources – Quantum Chemistry Application Use Case. In: Bubak, M., Szepieniec, T., Wiatr, K. (eds.) PL-Grid 2011. LNCS, vol. 7136, pp. 40–55. Springer, Heidelberg (2012)
Benedyczak, K., Stolarek, M., Rowicki, R., Kluszczyński, R., Borcz, M., Marczak, G., Filocha, M., Bała, P.: Seamless Access to the PL-Grid e-Infrastructure Using UNICORE Middleware, ibid, pp. 56–72
Dziubecki, P., Grabowski, P., Krysiński, M., Kuczyński, T., Kurowski, K., Piontek, T., Szejnfeld, D.: Online Web-Based Science Gateway for Nanotechnology Research, ibid, pp. 205–216
Kocot, J., Szepieniec, T., Haręźlak, D., Noga, K., Sterzel, M.: InSilicoLab – Managing Complexity of Chemistry Computations, ibid, pp. 265–275
InSilicoLab – an application portal supporting in silico experiments on e-Infrastructures, http://insilicolab.cyfronet.pl/
Jmol: an open-source Java viewer for chemical structures in 3D, http://www.jmol.org/
Open Babel: the Open Source Chemistry Toolbox, http://openbabel.org
Polish GRID Certification Authority, http://plgrid-ca.pl
gLite: Middleware for Grid Computing, http://glite.web.cern.ch/glite/
Romańczyk, P.P., Noga, K., Radoń, M., Rotko, G., Kurek, S.S.: On the role of noncovalent interactions in electrocatalysis. Two cases of mediated reductive dehalogenation, Electrochim. Acta 110, 619–627 (2013)
Eilmes, A.: Spiropyran to Merocyanine Conversion: Explicit versus Implicit Solvent Modeling. J. Phys. Chem. A 117, 2629–2635 (2013)
Niedoida: general purpose computational chemistry package, http://www.chemia.uj.edu.pl/~niedoida/
Mazur, G., Makowski, M.: Development and Optimization of Computational Chemistry Algorithms. Computing and Informatics 28, 115–125 (2009)
Mazur, G., Włodarczyk, R.: Application of the Dressed Time-Dependent Density Functional Theory for the Excited States of Linear Polyenes. J. Comp. Chem. 30, 811–817 (2009)
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Eilmes, A., Sterzel, M., Szepieniec, T., Kocot, J., Noga, K., Golik, M. (2014). Comprehensive Support for Chemistry Computations in PL-Grid Infrastructure. In: Bubak, M., Kitowski, J., Wiatr, K. (eds) eScience on Distributed Computing Infrastructure. Lecture Notes in Computer Science, vol 8500. Springer, Cham. https://doi.org/10.1007/978-3-319-10894-0_18
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DOI: https://doi.org/10.1007/978-3-319-10894-0_18
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