Perspectives of 1,4-DHP-lipid molecular dynamics
2013
Duka, V., Latvia Univ. of Agriculture, Jelgava (Latvia);Latvian Inst. of Organic Synthesis, Riga (Latvia) | Czaplewski, C., University of Gdansk (Poland) | Liwo, A., University of Gdansk (Poland) | Duburs, G., Latvian Inst. of Organic Synthesis, Riga (Latvia) | Liepina, I., Latvian Inst. of Organic Synthesis, Riga (Latvia) | Zeidmane, A., Latvia Univ. of Agriculture, Jelgava (Latvia)
This paper focuses on software aided methodology of molecular dynamics using classical modelling cycle that can be used for investigation of complex lipid system molecular dynamics such as the cationic amphiphilic lipid type compound 1,1’-\{[3,5-bis(dodecyloxycarbonyl)-4-phenyl-1,4-dihydropyridin-2,6-diyl]dimethylene\} bispyridinium dibromide (1,4-DHP lipid). We summarized and systematized the molecular dynamics simulation process, and provided a list of software tools that can be successfully used for different purposes in different steps of molecular dynamics simulation. We show that molecular dynamics simulation as a computer modelling method complies with the assumptions of the mathematical modelling cycle. That was proved with the successful molecular dynamics studies of 1,4-DHP lipid system. The cycle of 1,4-DHP lipid system modelling was accomplished with the verification of results, that is excellent result although it opens a perspectives for further analysis of this system.
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