nstance) VMD:
<pre>
vmd -m lig1.pdb lig3.pdb lig1_box.pdb
vmd -m lig1.pdb lig3.pdb protein_scoop.pdb water.pdb
</pre>
<img src="setup_free.png" width="221" height="200" alt="" /> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <img src="setup_bnd.png" width="219" height="212" alt="" />
</p>
<p> 
<h5>Execution</h5>
To run the bound and free legs of the simulation you need to execute
<pre>mpirun -np 16 $PROTOMSHOME/protoms3 run_bnd.cmd
mpirun -np 16 $PROTOMSHOME/protoms3 run_free.cmd
</pre>
This is most conveniently done on a