Phi-Psi Map Lesson, Introduction

In the lesson on generating a phi/psi map, you will explore how to set up a repetitive calculation with the Discover_3 module in the Insight interface. Polypropylene--(CH₂CH(CH₃))_n--as a bulk polymer prefers a gauche conformation about the C-C bond. The lowest-energy conformation for a C-C bond in a chain is the trans conformation, but the steric interaction of the methyl groups destabilizes it enough in polypropylene that the gauche conformation has the lowest energy.

In this exercise you will generate the potential energy surface for a small segment of the polymer chain as a function of the two torsion angles in the chain. The contour map of such a surface is useful both for understanding the possible conformations and flexibility of such a system and also as a test of the accuracy of a forcefield.

The commands in the Discover_3 module support a concept of stages of a calculation. Each stage sets up a distinct step of the calculation. To generate the phi/psi map, you need to obtain the energy at a grid of points. You will accomplish this by setting up a pair of nested loops over the two torsion angles. Since a rigid rotation about the torsions would not allow the molecule to relax and would result in an artificially high steric energy, you will need to minimize the structure at each grid point, applying a restraint so that the two torsion angles cannot change. Although this may sound complex, it is quite straightforward. These are the steps needed:

Loop from -180 degrees to +180 degrees for the first torsion
- Set the first torsion to the desired angle
- Add a restraint to keep it at the desired angle
- Loop from -180 degrees to +180 degrees for the second torsion
  - Set the second torsion to the desired angle
  - Add a restraint to keep it at the desired angle
  - Minimize the structure
  - Write out the structure and energy for later analysis
- End loop over second torsion
End loop over first torsion

Ordinarily, you need to build a segment of the polymer first. But we have supplied molecule-specification file for 2,4-dimethylpentane, as the model to be used in this lesson.

The main topics covered in this lesson include:

Additional topics include:

Phi-Psi Map Lesson, Instructions

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