Possible fix for velocity-less trajectories

I think this will fix some of the problems I've been dealing with; if it makes sense to you, then once you merge this PR into your master, it will be included as a part of https://github.com/choderalab/msm-tis/pull/49, and that will be ready to be merged into choderalab/master! (I know; it probably would have been easier for me to just tell you the lines to change in the discussion on choderalab#49, although I guess that in principle something like this is the right way to do it....)