Is there any way to change the size of preallocate data file in mongodb?
There is no way to specify your own sizes, the only way to alter the sizes of data files is to specify (or not) the smallfiles option.  That will bring the file sizes down to 25% of the default (max of 512MB rather than 2GB etc.)

You can pre-allocate the files yourself in advance (with dd, fallocate or similar).  I have a sample bash script using fallocate for just such a purpose here on GitHub. You still have to do the progression of sizes up to 2GB first, then allocate the remainder at 2GB though.  If nothing else, full pre-allocation would let you determine if allocation is having any kind of impact on your testing.