Speaker
Dr
Emanouil Atanassov
(Institute of Information and Communication Technologies, Bulgarian Academy of Sciences)
Description
A new class of compounds, the large-ring cyclodextrins (LR-CDs), attracted attention in recent years, and advances were marked in the study of their physicochemical properties in spite of existing difficulties in their synthesis, isolation and purification. Practical applications were also reported of this new class of compounds. Understanding the mechanism of their action requires knowledge of the macroring conformational dynamics. In view of the difficulties with the experimental examination of the conformations of LR-CDs, computational modeling and simulation methods provide useful tool to gain information about their conformational dynamics, the energetics, and the complex-forming ability.
Using molecular dynamics simulations as a conformational search protocol, post-processing of the simulation trajectories is carried out by: (i) the MM/GBSA (Generalized Born/Surface Area (LCPO)) methodology in order to estimate energy data, and (ii) principal component analysis (PCA), also called quasiharmonic analysis or essential dynamics method. With the methodology used we can monitor the concerted motions of the atoms of the molecule in a few dimensions, making it easier to visualize and investigate these motions. After examining the conformational interconversions in some lower-size LR-CDs (CDn, n=10, 11, …, 30),1-3 our efforts are focused now on treating problems with much higher dimensionality, e.g. CD100, as well as on inclusion complexes of LR-CDs. Due to the access to more powerful computational resources and parallelized software it became practically feasible to execute molecular dynamics conformational searches with longer duration for large cyclodextrins examined by us earlier with very short simulations, 5.0 ns (CDn, n=40, 55, 70, 85, 100; Giant cyclodextrins).4
Such studies require enormous computational resources and it is of crucial importance to make the proper choice of optimal hardware, as well as software configurations in order to execute the computations efficiently. We present in this report results produced at the HPC cluster at IICT-BAS with Infiniband interconnection, which is part of the HP-SEE infrastructure. All tests are in support for optimal execution of the specifically parallelized module PMEMD of AMBER v.11 with 64 cores on eight nodes.
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1 M. Gotsev, P. Ivanov, J. Phys. Chem. B, 2009, 113, 5752-5759.
2 P. Ivanov, J. Phys. Chem. B, 2010, 114, 2650-2659.
3 P. Ivanov, In: Current Physical Chemistry: Biomolecular Simulations and Applications, Vol. 2, 2012, in press.
4 P. Ivanov, C. Jaime, J. Phys. Chem. B, 2004, 108, 6261-6274.
Primary authors
Dr
Emanouil Atanassov
(Institute of Information and Communication Technologies, Bulgarian Academy of Sciences)
Prof.
Petko Ivanov
(Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences)
