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Unformatted text preview: Molecular Dynamics Simulations 2011 Exercise 11: Suggested solutions Eero Holmstr om November 30, 2011 1. To create and rotate the clusters, we modify the program created for Exercise 1 into the program makeclusters . The program creates two Cu clusters of userdefined diameter and distance from one another and rotates them by evenly distributed random Euler angles , , and (See Fig. 1). The rotation is performed using the rotation matrix R , so that r = Rr where R = cos cos  cos sin sin cos sin + cos cos sin sin sin  sin cos  cos sin cos  sin sin + cos cos cos cos sin sin sin  sin cos cos . Since again well be doing a series of runs, its best to write a script to do this for us ( runner_script ). So, whats going on in the simulations? Well, it looks like the two clusters coalesce to form a larger cluster of elongated form. This is because the system wants to saturate as many bonds as possible, or equivalently to minimize the...
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This note was uploaded on 02/14/2012 for the course CSE 6590 taught by Professor Kotakoski during the Winter '12 term at York University.
 Winter '12
 Kotakoski

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