 get a whole picture of where your waters were distributed throughout the simulation. To get a more visual picture of this we produce and visualize a water density file. To generate such a file run:
<pre>
python $PROTOMSHOME/tools/calc_density.py -f all.pdb -r wa1
</pre>
and the file grid.dx will be produced. Such a file can be visualized in vmd. Try looking at it with:
<pre>
vmd -m grid.dx ../protein.pdb ../fragment.pdb
</pre>
<p>
You should be looking at something similar to this (after fiddling a bit wit