RubyMine cannot recognize already installed gems

RubyMine version: 6.3

Ruby version: 2.3.3

bundler version: 1.15.1

Gem list:

activemodel (4.1.16)
activerecord (4.1.16)
activesupport (4.1.16)
arel (5.0.1.20140414130214)
ast (2.3.0)
bigdecimal (1.2.8)
builder (3.2.3)
bundler (1.15.1)
childprocess (0.7.0)
connection_pool (2.2.1)
cucumber (2.4.0)
cucumber-core (1.5.0)
cucumber-wire (0.0.1)
data_magic (1.0)
database_cleaner (1.3.0)
dbi (0.4.5)
deprecated (2.0.1)
did_you_mean (1.0.0)
diff-lcs (1.3)
domain_name (0.5.20170404)
facets (3.0.0)
factory_girl (4.4.0)
faker (1.7.3)
ffi (1.9.18 x86-mingw32)
fig_newton (0.14)
gherkin (4.1.3)
http-cookie (1.0.3)
http.rb (0.11.1)
i18n (0.8.4)
io-console (0.4.5)
jdbc-mysql (5.1.42)
json (1.8.6, 1.8.3)
json_spec (1.1.5)
mime-types (3.1)
mime-types-data (3.2016.0521)
minitest (5.10.2, 5.8.5)
multi_json (1.12.1)
multi_test (0.1.2)
net-http-persistent (3.0.0)
net-telnet (0.1.1)
netrc (0.11.0)
page-object (1.0.2)
page_navigation (0.10)
parallel (1.11.2)
parser (2.4.0.0)
pg (0.20.0 x86-mingw32, 0.18.4 x86-mingw32)
pickle (0.4.11)
power_assert (0.2.6)
powerpack (0.1.1)
psych (2.2.4, 2.1.0)
rainbow (2.2.2)
rake (12.0.0, 10.4.2)
RDee (0.4)
rdoc (4.2.1)
require_all (1.4.0)
rest-client (2.0.2 x86-mingw32)
rspec (3.6.0)
rspec-core (3.6.0)
rspec-expectations (3.6.0)
rspec-mocks (3.6.0)
rspec-support (3.6.0)
rubocop (0.49.1)
ruby-ole (1.2.12.1)
ruby-plsql (0.5.3)
ruby-progressbar (1.8.1)
rubyzip (1.2.1)
selenium-webdriver (2.42.0)
sequel (4.47.0)
spreadsheet (0.9.9)
test-unit (3.1.5)
testgen (0.9)
thor (0.19.4)
thread_safe (0.3.6)
tzinfo (1.2.3)
unf (0.1.4)
unf_ext (0.0.7.4 x86-mingw32)
unicode-display_width (1.2.1)
useragent (0.10.0)
watir-webdriver (0.6.11)
webdriver-user-agent (7.4)
websocket (1.0.7)
yml_reader (0.7)

I was using Ruby 2.1.9 before, and my bundler was working as expected. After updating my Ruby to 2.3.3. my bundler stopped working from RubyMine. I was able to use comandline to install all the gems in my gemfile using 'bundle install' command. Still RubyMine would not recognize the gems in SDK. The gems are all highlighted as they have not been installed. Also the gems are missing in the External Library as well. Again I did not have these issues when I had Ruby 2.1.9. 

After this I installed Intellij and added Ruby plugin, configured Ruby SDK, and all the gems got recognized by Intellij, and I am able to run my scenarios as expected.