I know what you are asking, but you are a little confused- Anakin was already fully turned to the dark side when he Force-Choked Padme on the Mustafar system-he even had to do his best to answer to " Anakin"- once you turn to the dark side, you answer to your Sith Name only.
Anyways Obi-Wan confronted Padme at their apartment on Coruscant if you recall and told her what Anakin had done, and found out that Anakin and her were married and expecting a baby - He asked her to tell him where Anakin was, Padme being smart said " You're going to kill him? arent you?" Obi-Wan" I have no choice"-Padme: " I cant tell you". Being concerned and wanting to know the truth Padme went to the Mustafar system to confront "Anakin" now full-fledged Darth Vader ( which means Dark Father), and he lied and told her to have faith in their love only, then he went and said " I am doing this for us, I am the most powerful in galaxy Padme together we can rule it" - Padme wanted democracy in the Senate, so she couldn't believe what she was hearing and said " Obi-Wan was right, you changed "- Anakin got mad and said " I don't want to hear anymore about Obi-Wan" . Then behind them Obi-Wan appeared on Padme's ship, he snuck on board so he could confront Anakin. Thinking this was Padme's idea and that she now loved Obi-wan, he force-choked her. The Dark Side was already so strong with him he forgot about his infant and he blamed Obi-Wan for her turning on him.
That's why when on Polis Massa, when Padme unexpectedly gave birth to twins, they had to be hidden and separated, and Padme died from a broken heart.
Well Anikan thought that Padme Amidala had lead Obi Wan to him so he could kill him so he choked Padme Amidala. He wasn't fully evil until The Empire Strikes Back. Padme didn't believe Anikan about her dieing so he also felt betrayed. The actual reason Padme died is that she had lost the will to live since Anikan had killed Jedi and children and was on The Dark Side. Him being on the Dark Side was the opposite of her so she was hurt mentally.