Influence of Ion Parameters On Molecular Dynamics and/or Free Energy Calculation

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Title in English	Influence of Ion Parameters On Molecular Dynamics and/or Free Energy Calculatio
Authors	FADRNÁ Eva KOČA Jaroslav ŠPONER Jiří
Year of publication	2005
Type	Article in Proceedings
Conference	Workshop on Modelling interactions in Biomolecules II
MU Faculty or unit	Faculty of Science
Citation
Field	Biophysics
Keywords	molecular dynamics simulations; human telomere; free energy
Description	Molecular modeling studies of DNA quadruplexes by means of several computational approaches including ns-scale MD simulation, Locally Enhanced Sampling and MM-PBSA. Simple model of ion description influences entire potential energy surface and may shift the molecule from experimental geometry. A lot of attention should be paid to force-field adjustment in order to reach true picture of the structure.
Related projects:	Proteins in metabolism and interaction of organisms with the environment