Abstract
Earlier, normalization conditions for the columns of the PCM (Polarized Continuum Model) were determined and a method of enlarged surface meshes was developed. We developed similar methods for the COSMO (COnductor-like Screening MOdel). These methods make it possible to introduce larger surface meshes without loss of accuracy and perform fast calculations of the solvation energy and the Born radii in the SGB (Surface Generalized Born) method. In addition, the corrections proposed in this work provide a significant enhancement in the accuracy of numerical calculations.
Similar content being viewed by others
References
M. Totrov and R. Abagyan, Biopolymers (Peptide Sci.) 60, 124 (2001).
A. Klamt and G. Schuurmann, J. Chem. Soc., Perkin Trans. 2, 799–805 (1993).
J. Tomasi and M. Persico, Chem. Rev. 94, 2027 (1984).
O. Yu. Kupervasser, S. N. Zhabin, and V. B. Sulimov, “DISOLV,” Certificate of State Registration Programs on the Computer, No. 2010612994 (2010).
O. Yu. Kupervasser, S. N. Zhabin, and V. B. Sulimov, “in Proceedings of II All-Russia Conference on Multiscale Simulation of Processes and Structures in Nanotechnologies, 27–29 May, 2009, p. 230.
O. Yu. Kupervasser, S. N. Zhabin, Ya. B. Martynov, K.M. Fedulov, I. V. Oferkin, A. V. Sulimov, and V. B. Sulimov, Vychisl. Metody Program. 12, 246 (2011).
J. R. Shewchuk, An Introduction to the Conjugate Gradient Method Without the Agonizing Pain, Technical Report (School of Computer Sci., Carnegie Mellon University, 1994), p. 58.
A. N. Romanov, S. N. Jabin, Y. B. Martynov, A. V. Sulimov, F. V. Grigoriev, and V. B. Sulimov, J. Phys. Chem. A 108, 9323 (2004).
D. V. Beklemishev, The Couse of Analytical Geometry and Linear Algebra (Nauka, Moscow, 1984), p. 319 [in Russian].
Author information
Authors and Affiliations
Corresponding author
Additional information
Original Russian Text © O.Yu. Kupervasser, I.P. Kikot’, 2011, published in Khimicheskaya Fizika, 2011, Vol. 30, No. 10, pp. 86–93.
An erratum to this article can be found at http://dx.doi.org/10.1134/S1990793112660013.
Rights and permissions
About this article
Cite this article
Kupervasser, O.Y., Kikot’, I.P. Enlarged surface meshes and normalization conditions for columns and rows of matrices in the COSMO method. Russ. J. Phys. Chem. B 5, 873–879 (2011). https://doi.org/10.1134/S199079311109020X
Received:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S199079311109020X