When you save a multiple plots/subfigures figure as an eps, the bounding box might not be properly defined. People who use pdflatex need to convert EPS to PDF. The undefined bounding box will cause problems if you use epstopdf to convert EPS to PDF. If you try
epstopdf --exact bad.eps
It will probably generate an warning msg like “Warning: BoundingBox not found!” and the resulting pdf is still wrong. One way to fix this problem is to use epstool
epstool --copy --bbox bad.eps --output good.eps
The –bbox option tells epstool to generate a (correct) bounding box for the eps file. With a correctly defined bounding box, you can easily convert an eps file to a pdf file.
epstopdf --exact good.eps