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Both the operating systems are installed side by side on my computer. The Windows hard drive mounts as an external hard drive on running Linux and I can access all the Windows files, as you'd know.

So is it possible to run Mathematica from the terminal or any other way? It will be very useful if possible.

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You definitely need some kind of virtualization software. If the copy of mathematica running on windows would be on another computer I would suggest using remote kernel. –  Wizard Jul 26 '13 at 9:34
I think you cannot because Windows binaries are not compatible with Linux and directory structure also varies. Better use Virtual Machine, that's what I do. Windows VM on host Linux. –  Rorschach Jul 26 '13 at 9:35

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