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Unformatted text preview: Molecular Dynamics Simulations 2011 Exercise 7: Suggested solutions Eero Holmstr¨ om November 2, 2011 1. The pressure control was implemented in main.c/f90 , and the virial calcula tion is done in forces.c/f90 . So, first we run the simulation with the usual atoms.in to get the equilibrium box size, which is found to be ∼ 18.833 ˚ A. Then we take the last frame of atoms.out , and scale all the coordinates by 1.02. This can be done with the following command (on a single line): tail 502 atoms.out  awk ’BEGIN{s=1.02} {if($1=="Cu"){print $1, $2*s, $3*s, $4*s, $5} else {print $0} }’ > atoms.in.2 Also, we must set the correct box size in mdmorse.in , which is 1 . 02 × 18 . 833. Then we run the simulation using the file atoms.in.2 as the input atom coordinates. And similarly for the case where we scale all coordinates by 0.98. Results are plotted in Figs 1 and 2. In Fig. 1 we have the box size in the xdirection (the same as in y and z due to symmetry) as a function of time. We see that for both cases the same equilibrium box size is found. It’stime....
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 Winter '12
 Kotakoski
 Thermodynamics, ........., molecular dynamics simulations, box size, Eero Holmstrom, equilibrium box size

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