From the GNU GPL FAQ:
If I write a plug-in to use with a GPL-covered program, what requirements does that impose on the licenses I can use for distributing my plug-in?
It depends on how the program invokes its plug-ins. If the program uses fork and exec to invoke plug-ins, then the plug-ins are separate programs, so the license for the main program makes no requirements for them.
If the program dynamically links plug-ins, and they make function calls to each other and share data structures, we believe they form a single program, which must be treated as an extension of both the main program and the plug-ins. This means you must license the plug-in under the GPL or a GPL-compatible free software license and distribute it with source code in a GPL-compliant way.
If the program dynamically links plug-ins, but the communication between them is limited to invoking the ‘main’ function of the plug-in with some options and waiting for it to return, that is a borderline case.
So it really depends on what "plugin" means in your case.
Now, you say that you are the author of the original software. As this was part of your PhD work, you may need to clarify who is the copyright owner for the software you wrote (often, the university is the copyright owner). If you are considered to be the copyright owner, then the GPL license doesn't restrict you in any way (supposing you are not depending on any GPL'd library).
Your question also seems to indicate that you are not completely done with your PhD. If you are still in university, you might have the power to change the license of your software (you need to check this with your supervisor / university staff). You could then just add a specific exemption from the GPL for linking with plugins.