If your journal does not submit to PubMed Central for authors, you will probably have to self-submit to PMC via the NIHMS. If multiple PIs or authors are involved, one should be designated as corresponding and submitting author.
Read your publisher's author agreement
Before submission, authors need to determine any stipulations journals may have placed on submission by authors. These stipulations can be found on the publisher's copyright agreement form or on the publisher's web pages for submission.
This form will often have a section dedicated to funding. If the agreement has such a section, make sure you indicate that you are NIH funded, and provide the grant numbers, if there is a field for them.
Journals may have other requirements or stipulations in author agreements such as:
Look for these stipulations in the author instructions page at the journal's site, or look up your journal in the JISC Open Policy Finder (link below).
Copyright Concerns
It is important to address copyright issues before depositing a manuscript to the NIH Public Access Manuscript Submission system (NIHMS).
If you have signed a contract with a publisher transferring ALL rights to your manuscript to them, you may have to obtain permission to submit your manuscript to NIH for public access. Authors are urged by NIH to avoid signing such agreements, since they will not allow the author to comply with the policy.
The NIH provides sample language to request in future copyright agreements with journal publishers:
"Journal acknowledges that Author retains the right to provide a copy of the final manuscript to the NIH upon acceptance for Journal publication, for public archiving in PubMed Central as soon as possible but no later than 12 months after publication by Journal."
NOTE: This statement will be updated to reflect the change in the policy to immediate access in PubMed Central. We will update this guide accordingly at that time.
In most cases, journals will not impede you from depositing manuscripts to comply with the policy, but on rare occasions, If an author has submitted a manuscript to the NIH Public Access system that is copyrighted to a journal, the journal may request to have the material removed from the Public Access system.
For other information on copyright issues, please consult the NIH Policy's copyright page.
Please be aware that these are suggestions and guidelines as recommended by the NIH policy pages. They are not intended to be interpreted as legal counsel.
(retrieved from https://www.nihms.nih.gov/login/?next=/submission/#process)