Hi Dan,
I figured that there is a deep underlying reason for that behavior :-)
The problem is, that when the number of frames in the input trajectory and
the number of data points in the data set dont match, cpptraj still produces
seemingly valid results (and there are no warnings, one has to carefully
check the size info after "DATASETS:")
So when the number of input datapoints Np is larger than the number
trajectory frames Nf, then only Nf result lines are produced. What is in my
eyes even more critical, when Nf > Np, I get Nf result lines with numbers
which look ok, but are obviously drawn out of thin air - at least I havent
recognized a pattern where they come from...
Thanks for looking into that,
Th.
Gesendet: Mittwoch, 01. März 2017 um 17:26 Uhr
Von: "Daniel Roe" <daniel.r.roe.gmail.com>
An: "AMBER Mailing List" <amber.ambermd.org>
Betreff: Re: [AMBER] cpptraj: dihcovar and projection need trajin to work
properly?
Hi,
This behavior occurs because of the way cpptraj (like ptraj before it)
is set up to handle 'Actions'. By definition, an 'Action' is something
that operates on input trajectory frames, which is why the 'matrix'
Action requires input trajectory frames. In reality the construction
of matrices from derived data (like dihedral covariance, IRED, etc)
should be an 'Analysis', but is in the 'matrix' Action for historical
reasons.
I should probably create an Analysis called 'buildmatrix' or something
for creating matrices from derived data in this manner. I'll open up
an issue on GitHub and try to get to it ASAP.
Thanks for the report! Let me know if anything is unclear or if you
have more questions.
-Dan
On Tue, Feb 28, 2017 at 10:33 AM, Thomas Fox <thomas_fox.gmx.net> wrote:
>
> Hi,
>
> I found a cpptraj behavior that I think is at least unintuitive:
>
> From a previous cpptraj run, I have a data set of dihedrals which I would
> like to further process in a separate cpptraj run.
> So I use the "readdata" and "dataset mode torsion" commands followed by
> "matrix dihcovar dihedrals".
> However, unless I have read in a structure with trajin before (a single
> frame is enough, no matter how large my data set is),
> the size of the resulting matrix is 0.
>
> I find this weird, as I dont need the parm or trajin info - I exclusively
> work on the data set I got from readdata.
> The same is true for the projection command...
>
> Ah, and this occurs both with Amber16 cpptraj and with the (current?)
> cpptraj (it says version V17.00b) I got from github.
>
> I have attached my cpptraj input file as well as the dihedral data file
and
> the output files for the two cases.
>
> Best,
> Th.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> [1]http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
[2]
https://www.lobos.nih.gov/lcb
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References
1.
http://lists.ambermd.org/mailman/listinfo/amber
2.
https://www.lobos.nih.gov/lcb
3.
http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Mar 01 2017 - 10:00:02 PST
