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SUMMARY:Efficient Parallel Simulations of Large-Ring Cyclodextrins on HPC 
 cluster
DTSTART;VALUE=DATE-TIME:20121019T103000Z
DTEND;VALUE=DATE-TIME:20121019T110000Z
DTSTAMP;VALUE=DATE-TIME:20261011T091831Z
UID:indico-contribution-195@indico.ipb.ac.rs
DESCRIPTION:Speakers: Emanouil Atanassov (Institute of Information and Com
 munication Technologies\, Bulgarian Academy of Sciences)\nA new class of c
 ompounds\, the large-ring cyclodextrins (LR-CDs)\, attracted attention in 
 recent years\, and advances were marked in the study of their physicochemi
 cal properties in spite of existing difficulties in their synthesis\, isol
 ation and purification. Practical applications were also reported of this 
 new class of compounds. Understanding the mechanism of their action requir
 es knowledge of the macroring conformational dynamics. In view of the diff
 iculties with the experimental examination of the conformations of LR-CDs\
 , computational modeling and simulation methods provide useful tool to gai
 n information about their conformational dynamics\, the energetics\, and t
 he complex-forming ability.\nUsing molecular dynamics simulations as a con
 formational search protocol\, post-processing of the simulation trajectori
 es is carried out by: (i) the MM/GBSA (Generalized Born/Surface Area (LCPO
 )) methodology in order to estimate energy data\, and (ii) principal compo
 nent analysis (PCA)\, also called quasiharmonic analysis or essential dyna
 mics method. With the methodology used we can monitor the concerted motion
 s of the atoms of the molecule in a few dimensions\, making it easier to v
 isualize 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 dime
 nsionality\, e.g. CD100\, as well as on inclusion complexes of LR-CDs. Due
  to the access to more powerful computational resources and parallelized s
 oftware it became practically feasible to execute molecular dynamics confo
 rmational searches with longer duration for large cyclodextrins examined b
 y us earlier with very short simulations\, 5.0 ns (CDn\, n=40\, 55\, 70\, 
 85\, 100\; Giant cyclodextrins).4\nSuch studies require enormous computati
 onal resources and it is of crucial importance to make the proper choice o
 f optimal hardware\, as well as software configurations in order to execut
 e 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 e
 xecution of the specifically parallelized module PMEMD of AMBER v.11 with 
 64 cores on eight nodes. \n___________________\n1 M. Gotsev\, P.  Ivanov\,
  J. Phys. Chem. B\, 2009\, 113\, 5752-5759.\n2 P. Ivanov\,  J. Phys. Chem.
  B\, 2010\, 114\, 2650-2659. \n3 P. Ivanov\,  In: Current Physical Chemist
 ry: Biomolecular Simulations and Applications\, Vol. 2\, 2012\, in press.\
 n4 P. Ivanov\, C. Jaime\, J. Phys. Chem. B\, 2004\, 108\, 6261-6274.\n\nht
 tps://events.saifa.rs/event/291/contributions/195/
LOCATION:National Library of Serbia
URL:https://events.saifa.rs/event/291/contributions/195/
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