Method A: Publish in a journal that deposits all final published articles in PubMed Central (PMC) within 12 months of publication and without author involvement. By far the easiest submission avenue available; see a list of journals that will do this for you. Make sure the publisher has your NIH grant number!
Method B: Make arrangements to have the publisher deposit a specific final published article in PubMed Central.
Method C: Deposit the final peer-reviewed manuscript in PubMed Central yourself via the NIH Manuscript Submission System (NIHMS).
This step requires more legwork on your behalf. You will submit your paper to the NIHMS and eventually PMC; it takes three steps:
Method D: Complete the submission process for a final peer-reviewed manuscript that the publisher has deposited in the NIH Manuscript Submission System (NIHMS).
Log into the NIH Manuscript Submission System using your eRA Commons login. (If you are a researcher and don't have a login, learn how to register for one). If you are submitting a manuscript on behalf of someone else, you may login to the system and submit using your My NCBI account. See image below for a snapshot of what you will see before you login to the system.
Use caution when selecting a grant to associate with an article - contact the Principal Investigator (PI) if you are unsure.