 the ProtoMS command file for the gas-phase simulation</li>
</ul>
You can read more about the command files in the ProtoMS manual. However, some sections of it are worth mentioning here
<p>  
<pre>
lambdare 100000 0.000 0.067 0.133 0.200 0.267 0.333 0.400 0.467 0.533 0.600 0.667 0.733 0.800 0.867 0.933 1.000
</pre>
<br>
this section, which exists in all input file setup the &lambda;-replica exchange. You can add more &lambda;-values manually if there are regions where the simulation is not performing well.
