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In the command files for dual-topology simulations, the following lines exist<br>
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<pre>
dualtopology1 1 2 synctrans syncrot
softcore1 solute 1
softcore2 solute 2
softcoreparams coul 1 delta 0.2 deltacoul 2.0 power 6 soft66 
</pre>
this section, which exists in both input files, sets up the dual topology simulation with appropriate soft-core parameters. It could be worth trying to optimize the soft-core parameters if your simulation is not performing well. 

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