md2011-09-note_Part_1

md2011-09-note_Part_1 - Molecular Dynamics simulations...

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Molecular Dynamics simulations Lecture 09: Molecular Mechanics / ReaxFF Dr. Olli Pakarinen Original lecture notes by Dr. Jani Kotakoski, 2010 University of Helsinki Fall 2011 CONTENTS Molecular mechanics (MM) Force fields for molecular interactions Force field approach in MD I GROMACS I ReaxFF
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Molecular Mechanics I Molecular mechanics (MM) is a method to describe complex molecular systems I Structurally there are two differences between MD and MM: I The constituent particles are molecules or parts of molecules rather than single atoms I Interactions are typically described via force fields instead of potentials I For example, methyl (–CH 3 ) and methylene (–CH 2 ) groups are often modeled as single entities I Also, large proteins are sometimes modeled as a set of attached beads I Bonds are presented as springs – no bond breakings occur I However, the prototypical application is simple energy minimization, not time evolution – different optimization methods I However, many variations exist Force Fields I
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md2011-09-note_Part_1 - Molecular Dynamics simulations...

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