Hi rajeev,
I did some research for you, and it appears you will need to use an OpenCart extension in order to have the OpenCart login appear in a popup window.
You could update your template so that the "Login" link opens in a new window, but that would still show all of the other text on the page. I am assuming that you are looking for a cleaner login page, a smaller one that looks nice in a popup.
The closest extension I found is:
Pop-up Login AJAX Window for OC v1.5.x
On that page is a link to a YouTube video that shows you exactly how the extension works.
I hope this points you in the right direction. Feel free to post a comment at the bottom of this page if you have any additional questions.
Thanks,
- Brad