Projects / Programmes source: ARIS

Computer Simulation of Structure and Dynamics of Proteins

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Research activity

Code Science Field Subfield
1.07.03  Natural sciences and mathematics  Computer intensive methods and applications  Simulations 

Code Science Field
P000  Natural sciences and mathematics   
P170  Natural sciences and mathematics  Computer science, numerical analysis, systems, control 
Keywords
Simulations, Algorithms, Molecular Dynamics, Symplectic Methods, Harmonic Analysis
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Organisations (1) , Researchers (5)
0104  National Institute of Chemistry
no. Code Name and surname Research area Role Period No. of publications
1.  08329  PhD Simona Golič Grdadolnik  Chemistry  Researcher  1998 - 2001  340 
2.  02287  PhD Milan Hodošček  Chemistry  Researcher  1996 - 2001  289 
3.  06734  PhD Dušanka Janežič  Computer intensive methods and applications  Head  1996 - 2001  507 
4.  08611  PhD Janez Mavri  Chemistry  Researcher  2000 - 2001  384 
5.  06431  PhD Ksenija Poljanec  Chemistry  Researcher  1996 - 2001  27 
Abstract
A new, explicit, symplectic integration algorithm for molecular dynamics simulation will be developed. The method is based on splitting of the total Hamiltonian of the system into the harmonic part and the remaining part in such a way that both parts can be efficiently computed. The algorithm will allow an integration time step up to an order of magnitude larger that can be used by other methods of the same order. This should significantly extend the scope of the presently used algorithms and thus contribute to the general applicability of molecular dynamics. The algorithm will be applied to some biologically interesting examples.
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