Previous behavior:

1. If -o was not specified, it would set the out_file to whole.xtc
2. If -x was not specified, it would set the trajectory to -f, and -o to whole.gro, regardless of whether -o was already set

This resulted in a bug when -o was specified but -x was not, since it would write to whole.gro anyway

New behavior:

1. If -o is not specified, set out_file to None
2. If -x is not specified, set trajectory to the file specified in -f
3. If out_file is None, use a filename "whole" with the extension that matches trajectory