Simulaid tutorial

Simulaid: utilities for setting up simulations and for the analysis of structures and simulation trajectories.

Simulaid description/documentation:

To execute Simulaid on Minerva, at the login prompt type

For analyzing a single protein structure, download one from the PDB or use one you already have. If there are no hydrogens, add them, e.g., with OpenBabel.

For analyzing trajectories, there is a trajectory and the corresponding structure file in ~mezeim01/molmod_course/md:

The trajectory contains 25,000 snapshots. Most analyses are fast (minutes at most). The exception is the generation of the 2D-RMSD.

To run the 2D-RMSD calculation you can gain significant amount of time if you create a new trajectory that

This can be obtained through a trajectory 'conversion':
Last modified: 11/30/2017          Go to Mezei Lab Home page