
This tutorial provides a full example of a CpHMD simulation, including file
preparation, initialization, production and analysis. The model system is
hen egg white lysozyme (as obtained from the PDB file 4lzt.pdb), which is
simulated in water at pH 7.0.

Follow these steps:

1. Go to directory initial. Follow the instructions in file INSTRUCTIONS.

2. Go to directory CpHMD. Follow the instructions in file INSTRUCTIONS.

3. Go to directory analyses. Enter into each of its sub-directories and
   follow instructions in the file INSTRUCTIONS.

The INSTRUCTIONS files are written as shell scripts but, instead of running
them, you should execute each command individually on the terminal and
check the output at each step, reading the corresponding comments and
trying to understand what you are doing.

The indicated running times for some of the commands refer to a typical
Linux desktop computer (as of 2019).

After you are done with this tutorial you may experiment to change some
parameters (e.g., run CpHMD at a different pH), do other analyses,
etc. Overall, this is expected to give you a basic understanding of the
workflow of this CpHMD implementation, so that you can apply it to your own
systems.

