In order to get the greatest performance out of one's internal hard drive, one needs to do a few simple things. It will be helpful to have a phillips head screw driver, a partitioning program, and an anti-virus program in order to fully and truly optimize an internal hard drive. However, there is one piece of advice that holds true for almost all internal hard drives: the more full they get, they slower they perform. The first step in achieving optimal hard disk performance should therefore be the elimination of any unnecessary files.
The screw driver will help only in the case of older IDE internal hard drives. Opening the case and discovering if the internal hard drive is on the same cable as an optical disk drive is the first chore. It pays to remember that in the case of old IDE configurations, the total speed is per channel, not per drive. This means that an internal hard drive sharing the same ribbon cable as an optical drive will see its performance severely degraded once one begins using the optical drive. In an ideal configuration, the optical drive would be on a different channel than the primary internal hard drive.
Newer SATA and SATA II internal hard drives do not have this limitation, but there may be performance problems if one is using an SATA II internal hard drive with an SATA connector. The newer standard allows for twice the speed as well as other improvements that can streamline random reads and writes more effectively, so it behooves one to find an add-in card that supports SATA II drives if this is the case. Be wary of inexpensive SATA II add-in cards as they may not deliver the full performance as promised by the specification itself, or worse yet they may not be bootable.
Having an up to date partitioning program is important for anyone that knows how to use it properly. It is important to back up all data before attempting to repartition any internal hard drive. Internal hard drives are basically magnetic platters spinning rapidly under a read/write head at a speed that is generally fixed. This means that the outer rims of each magnetic platter not only store the most data, but they are also the surface areas where data can be read and written the quickest. Set up a partition for the outer area of the drive large enough to host swap files or other speed sensitive data.
It is sad, but true: viruses are everywhere and they not only eat CPU time and memory, they also can be the cause of poor hard disk performance. There are plenty of free anti-virus applications on the market, so there really isn't any excuse not to at least use an anti-virus program to systematically sweep the internal hard drive and ensure that all is clear.
To summarize, the primary ways to keep an internal hard drive in tip top shape are: removing unnecessary files, don't let the interface be the limiting factor, partition when applicable and keep it virus free.
Source : www.goarticles.com by Matthew Kerridge

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