do this both with thermodynamic integration, Bennett's acceptance ratio (BAR) and multistate BAR (MBAR). To do this you can type</p>
<pre>
python $PROTOMSHOME/tools/calc_dg.py -d out_free/ -l 0.025
</pre>
<p>A typical result is between 0 and 1 kcal/mol. Notice that only 10 snapshots are removed from the 400 snapshots (2.5 % of the simulation) when calculating the free energy, because the analysis with <code>calc_series.py</code> indicated that the simulation was equilibrated very much from the start.</p>
<p