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It will depend upon the protocol you are using/writing.
For example, if you are going to improve existing version of AODV and make it to behave as Power Aware AODV then you have to do those modifications mainly in aodv.cc and aodv.h and other files in aodv folder of ns2 directory.
If you are writing your own protocol, then you have to write everything in your code and just need to do little modifications on some ns2 files (mostly, packt.h packet.cc, ns-lib.tcl, ns-default.tcl, Makefile etc.,) to integrate your protocol with ns2.
If you just want to change the default values of parameters such as tx power or rx power then you can do it in your tcl simulation code. If you want to change those values permanently, then you may set it in in
ns-allinone-2.xx/ns-2.xx/tcl/lib/ns-default.tcl or the files related with energy model of ns2.
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