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.
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