Fix trjconv modifying fr.time unnecessarily

The was a bug where trjconv modified the input frame time, which
caused issues with xtc seeking. This has recently been fixed
by commit 81d10b25, but it's better not to mess with the input
frame and only modify the output frame.

Refs #1405, #1406

Change-Id: Ibf7c8655e916c12f8cc51523a67556cc7988e6e6