Tutorial_5_5C2H6 - Oscar Tutorial 5 page 1 Tutorial 5:...

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page 1 Tutorial 5: Ethane Bond and Angle Vibrations; Torsional Rotations Ethane (C 2 H 6 ) is the smallest alkane molecule that offers a chance to investigate the oscillations in bond lengths and bond angles, as well as torsional rotations about a C-C bond. The C-H and C-C bonds have very high frequency vibrations, with periods on the order of a few tens of femtoseconds. (1 fs = 0.001 ps). The characteristic times for oscillations in the H-C-H and C-C-H bond angles are also in this same time range. In this tutorial, you will carry out an MD simulation on an all-atom model of five ethane molecules at a target temperature of 300K. As you will see, a 1 ps simulation is sufficient to investigate the behavior of bond lengths and bond angles. It will also provide us with a look at the behavior of the central H-C-C-H torsion. You will examine all these in more detail in Tutorial 6. The system contains five ethane molecules in a small box. You will run a constant energy simulation (no adjustment of temperature after assigning the initial velocities). The energy will be frequently redistributed between the various degrees of freedom by the collisions between the molecules, and by the collisions of each molecule with the wall of the box. You will work in teams of two, but each of you must run your own simulations, analyze your own data, and turn in your own plots. At least one member of each team should run the “Sim1” conditions, and at least one should run the “Sim2” conditions. There are two simulations, “Sim1” and “Sim2”. Conditions are identical for both except for the output interval and the total number of steps: Use the following settings: Coordinate file 5C2H6_equil.pdb Structure file 5C2H6.sf Job name xxx (use whatever you want here.) Output interval Sim1: 1 step Sim2: 5 steps Raw coordinates Off Time step 0.001 ps (default) Number of Steps
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This note was uploaded on 09/22/2011 for the course BIOL 7110 taught by Professor Steveharvey during the Spring '11 term at Georgia Institute of Technology.

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Tutorial_5_5C2H6 - Oscar Tutorial 5 page 1 Tutorial 5:...

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