The Documentation for nn.Conv2d suggests that:

In the first nn.Conv2d, 3 is the number of input channels, 6 is the number of output channels and 5 in the length of the kernel, assuming a square kernel. So your kernel is a [5,5] box.
In  the second nn.Conv2d, 6 is the number of input channels, 16 is the number of output channels and 5 is the size of the kernel.

More information available here: link 1