gmx traj needs reform
gmx traj does too many things that conflict with each other.
The xvg written by -av and -ax does not describe the Y axis adequately.
The implementations of things like -av and -cv are conflated to the point that you can't dump the average velocities of a group per frame to .xvg unless you provide a topology (because you need that for implementing -cv). Same for -af and -cf.
There should not be a distinct implementation of PBC handling in remove_jump.
The -vd option should probably not roll its own histogram implementation
#3 Updated by Teemu Murtola over 2 years ago
This should also be compared with
gmx trajectory. Probably some of the existing functionality in
gmx traj would fit there (I just put the bare minimum to support writing out trajectories from selections), but some of the existing options would probably better fit into a separate tool. And generic abilities like removing jumps would probably better go into the framework instead of individual tools.