[gmx-developers] [RFE] Converting velocities / parsing with trjconv

[Anton Feenstra]

Jay Mashl wrote:
> 
> I have been looking for a way to generate velocity trajectories and ran into
> some difficulties with trjconv. When nstvout > nstxout, there is a trivial hack
> to do this.
> 
> However, if the velocities have been saved more often than the coordinates
> (i.e., nstvout < nstxout), then the default trjconv semes to overlook those
> frames without a leading set of coordinates. Glancing at the source, it could
> be that the velocities are read as coordinates instead.

Hmm. that smells like a dirty bug...

> What are your thoughts on providing a sort of "-nogro" option in trjconv?  It
> might be nice to be able to split coordinate, velocity, and force trajectories
> into separate files, regardless of the values for nstvout, nstxout, nstfout.

I am not sure what you mean with '-nogro', but anyway, it should indeed
be possible to select an arbitrary subset of velocities, coordinates and
forces from a trajectory, regardless of the presence and frequency of any 
or all of them in the source trajectory.

The reason trjconv is the way it is now, is that it was written with a
'sensible' trajectory in mind, which is written only to allow a re-start
in emergency situations, i.e. nstxout <= nstvout <= nstfout, so there 
are either coordinate-only frames, or coordinate+velocity frames or 
coordinate+velocity+forces frames. Sensible support for forces may be 
lacking at all, since these are hardly ever used. This may not always be 
what a user wants or expects, so it is probably good to think this over...


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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