Medina, the Jewish City

here; It was founded by jews but, other arabic tribes were living there too.
And Mohammad didnt kill them:Look:
Muhammad's arrival
In 622, Muhammad left Mecca and arrived at Yathrib, an event that would transform the political landscape completely; the longstanding enmity between the Aws and Khazraj tribes was dampened as many of the two tribes embraced Islam. Muhammad, linked to the Khazraj through his great grandmother, was soon made on the chiefs and united the Muslim converts of Yathrib under the name "Ansar" (the Helpers). After Muhammad's arrival, the city gradually came to be known as Medina.

According to Ibn Ishaq, the Muslims and Jews of the area signed an agreement, the Constitution of Medina, which committed Jewish and Muslim tribes to mutual cooperation. The nature of this document as recorded by Ibn Ishaq and transmitted by ibn Hisham is the subject of dispute among modern historians many of whom maintain that this "treaty" is possibly a collage of agreements, oral rather than written, of different dates, and that it is not clear when they were made or with whom.[11]


Conflict with Meccans and Jews
In January of 623 Muhammad dispatched Obeida, son of Harith to lead another raiding party against a caravan passing along the Syria-to-Mecca trade route. As the caravan (led by Abu Sufyan) was watering in the valley of Rabigh, Muhammad's men fired volleys of arrows from a distance but did not inflict any damage. Obeida was given the honor of "he who shot the first arrow for Islam" as Abu Sufyan altered course to flee the highwaymen. In retaliation for this attack Abu Sufyan requested an armed force from Mecca who came and engaged in the Battle of Badr.

Throughout the winter and spring of 623 other raiding parties were sent by Muhammad from Medina but, while troublesome, were not particularly effective or destructive.

Muhammad's agreement with the Jewish tribes soon broke down, as the Jews would not accept Muhammad's claims to prophethood. After his victory at Badr, Muhammad besieged and conquered the tribe of the Banu Qaynuqa, that had been involved in a tribal feud and adamantly refused to convert to Islam. Because of the intercession of Abdallah ibn Ubayy, Muhammad spared tribe's lives and expelled them from the city.
----------------------------------------------------------------------------------------------------------------------------------------
But The they made a war again and then they killed the male memebers.Anyway, it is not good here mention all the conflicts..In the crusades thay killed a lot of muslims also(millions of them) if we tell here who did whom what, all the Atlantis forum will be full of wars.Sorry to say that, but please be Objective.