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Linux is a UNIX-like open source operating system with hundreds of distinct distributions, including: Fedora, openSUSE, Ubuntu, Debian, Slackware, Gentoo, CentOS, and Arch Linux. Linux is generally associated with web and database servers, but has become popular in many niche industries and applications.
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VMware Converter is a free application, and does it's best.
You may want to consider using a commercial application such as Platespin Migrate by NetIQ, which can convert some Linux Distributions from Physical to Virtual.
Which Linux Server distro, do you have ?