So I am in a situation where my 2 chains (2 proteins) from the same simulation are separately in 2 DCD files each having 2000 frames. I wanted to merge these 2 DCD files into single DCD file (which will have total 2000 frames) containing both chains. I know this might be possible in VMD. Can someone help me?
NOTE : I am not talking about concatenating DCD files (which is done using catdcd)
The ease with which you are able to do this depends on the format of the force field/topology you used. If you used Amber topology, then it's much more difficult, as Amber's format is very sensitive to having a 1-1 correspondence between atoms referenced in the topology and atoms in your structure. If you used CHARMM, then you can generate a psf file containing all the atoms of both frames.
Regarding the actual superposition/merging of the structures, you need to know exactly how to orient the two molecules relative to each other, especially if this is for any numerical analysis. If this is for display, then just load the two chains into VMD as separate atoms and show both at once.
I'm curious why you have two trajectories written in the first place -- do you have access to the original dcd output by NAMD?