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md-ex07 - Molecular Dynamics Simulations 2011 Exercise 7...

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Unformatted text preview: Molecular Dynamics Simulations 2011. Exercise 7: Pressure con- trol. Return by Tue 1.11. at 12:15, exercise session Thu 3.11. at 12:15. 1. (12 p) Implement Berendsen pressure control into mdmorse. Use the read-in parameters bpctau , desiredP , and bpcbeta . The first of these is the pressure control time constant τ P , the second one is the desired pressure towards which the pressure is scaled, and the third one is the compressibility β (1/bulk modulus) of the material. Implement the algorithm so that the control is not used at all if bpctau=0 . Implement a pressure / virial calcula- tion in the force routine and the control in the main routine. Use kbar as the external pressure unit. Mark the pressure-related modifications in the code with comments that contain the string “ bpc ”. Test your code in the following way. Set T = 300 K and P = 0. Find the equi- librium box size for the system by simulating for 10 ps with τ T = τ P = 300 fs. Then perform two simulations where the box size (in filefs....
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