I think you're confusing ulimit (a bash builtin) with pam_limits(8). Your question is about the former. The
/etc/security/limits.conf file is associated with the latter.
That said, one option you have is to provide the ulimit values you want via bash's startup file(s):
- /etc/profile (system-wide); or
- ~/.bash_profile (user-specific); or
- see the bash(1) manpages for others