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Unformatted text preview: Molecular Dynamics Simulations 2011. Exercise 8: Eﬀect of cut-oﬀ
radius and time step.
Return by Tue 8.11. at 12:15, exercise session Thu 10.11. at 12:15.
1. (10 p) Simulate a Cu FCC system with periodic boundary conditions at
a temperature of 300 K for 10 ps using mdmorse. Do the simulations with
the following values for the potential cut-oﬀ radius (rpotcut in mdmorse):
rc = 4.0, 4.5, 5.0, 6.0, 8.0 ˚. Investigate the energy conservation by calculatA
ing the average ﬂuctuation (variance or the like) in total energy. Remember
to skip say the ﬁrst 200 time steps from the beginning of the simulation when
calculating any averages.
Why do the ﬂuctuations behave as they do as a function of rc ? Hint: See
the ﬁgure below, where the pair correlation function g (r) of Cu at 300 K is
plotted. Also plotted is the Morse potential used in the simulations.
For all simulations, set the neighborlist cut-oﬀ radius (rskincut) to 1 A
larger than the potential cut-oﬀ. The default value of MAXAT*MAXNEIGHBORS
in modules.f90/global.h should be large enough. 2. (10 p) Investigate the eﬀect of the time step deltat on energy conservation in the code mdmorse. Use time steps of 1, 3, 10, 30, and 100 fs to
simulate thermal motion in Cu at 300 K for 10 ps. Plot the total energy as
a function of time for each time step in the range in which it still behaves
sensibly. What happens with the atoms for the largest time steps?
Return the appropriate ﬁgures and answers to the questions. ...
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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