Post-Processing Challenges in Simulations of Lipopolysaccharide Membranes and Aggregates
Resumo
Computer simulation of Gram-negative bacteria membrane is a computational intense task that requires massive parallel computing. In addition, these simulations require post-processing tools that are in general not parallelized. Here we comment on the types of parallelizable analysis tools and propose two new types of analyses that can be applied on such systems.
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Brandenburg, K. and Seydel, U. (1988). European Journal of Biochemistry 16, pages 83-87.
Brandenburg, K., Mayer, H., Koch, M. H., Weckesser, J., Rietschel, E. T. and Seydel, U. (1993). European Journal of Biochemistry 218, pages 555-559.
Brandenburg, K., Kusumoto, S. and Seydel, U. (1997). Biochimica et Biophysica Acta 1329, pages 183-201.
Hess, B., Kutzner, C., van der Spoel, D. and Lindahl, E. (2008). Journal of Chemical Theory Computation, 4, pages 435-447.
Kirschner, K. N., Lins, R. D., Maass, A. and Soares, T. A. (2012). Journal of Chemical Theory and Computation, 11, pages 4719-4731.
Kumar, A., Grupcev, V., Yuan, Y., Tu, Y-C. and Shen, G. (2012a). EDTB, pages 26-30.
Tu, Y-C., Chen, S., Pandit, S., Kumar, A. and Grupcev, V. (2012b). ACM Conference on Bioinformatics, Computational Biology and Biomedicine, pages 527-529.
Peterson, E. S. ; William, L. ; Stephan, E. R. ; Rose, S. ; Corrighan, A. ; Lai, C. ; Lins, Roberto D., Critchlow, T., Straatsma, T. P., Soares, Thereza A., Scarberry, R. (2008). BIOCOMP, pages 558-562.
Pontes, F. J. S., Rusu, V. H., Soares, T. A. and Lins, R. D. (2012). Journal of Chemical Theory and Computation, 8, pages 3830-3838.
Seydel, U., Oikawa, M., Fukase, K., Kusumoto, S. and Brandenburg, K. (2000). European Journal of Biochemistry, 267, pages 3032-3039.
Publicado
28/07/2014
Como Citar
SANTOS, Denys; RUSU, Victor; PONTES, Frederico; DIAS, Roberta; CUNHA, Keila; POL-FACHIN, Laércio; SOARES, Thereza; LINS, Roberto.
Post-Processing Challenges in Simulations of Lipopolysaccharide Membranes and Aggregates. In: BRAZILIAN E-SCIENCE WORKSHOP (BRESCI), 8. , 2014, Brasília.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2014
.
p. 69-72.
ISSN 2763-8774.
