 computer cluster. The calculations will take approximately 48 h to complete.
<p>
<h5>Analysis</h5>
When the simulations are finished you need to analyse the simulation and extract the free energy of the bound and free legs. We will start with looking at some energy series to investigate whether the simulations are converged. Type
<pre>
python $PROTOMSHOME/tools/calc_series.py -f out_free/lam-0.000/results
</pre>
to look at time series for the free leg at &lambda;=0.0. In the wizard that appears you can typ