 the free leg. Therefore, you also need to execute ProtoMS 10 times with the different input files. The output will be in 10 different folders, e.g. <code>out1_bnd</code> and <code>out2_bnd</code>.
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<h5>Running with temperature replica-exchange</h5>
To improve sampling, one could add temperature ladders to the simulation and perform replica-exchange swaps between neighboring values of temperatures. To add eight additional temperatures to &lambda;-values 0 and 1.0, add the following lines to the command f