This directory contains the minimum number of files for going through this 
exercise. When going through all the steps (not only the recommended ones) 
other files will be generated, and they will be massive. 
It is strongly encouraged to just use these files, as the production of 
the runs is also computationally expensive.
 
The file ubq-nvt.dcd is not present, because of its size, and thus step 2 
of this section of the tutorial can not be performed unless you run the 
NVT simulation. Nevertheless, it is useful to take a look at the script 
mk_protein_dcd.tcl in case you have to do something similar in the future.

NOTE! The file ubq-nvt-prot.dcd contains only ~200 ps, from 
time 400-600ps of the NVT simulation. In this time the protein appeared 
equilibrated, and thus studies in the fluctuation of the energy in this time 
frame are appropriate. The previous 400ps of simulation are not provided in 
order to save file space. 

