Part 4 - Measurement, Trajectories and Movement

The whole purpose of loading molecules into sire is that you can then do things with them. Typical things you may want to do could include;

• Measuring distances, angles or torsion angles between atoms, residue or molecules.

• Making measurements across multiple frames of a trajectory.

• Measuring energies of molecules or subsets of molecules, and across multiple frames of a trajectory.

• Moving atoms, residues or molecules, e.g. by direct translation and rotation of parts, or even by stretching bonds or rotating angles, and saving these to a trajectory.

• Performing energy scans by calculating the energy for different configurations of the molecule (e.g. a dihedral scan).

This chapter will teach you to do all of the above. Since measurement, trajectories and movement are easier if you can see molecules and create graphs, you will also learn how to visualise sire objects and data.

• Measuring Distances and Angles
• Measuring Trajectories
• Measuring Energies
• Measuring Energies Across Trajectories
• Moving Atoms and Molecules
• Moving Bonds, Angles and Dihedrals