Hi,
What you want to do is currently not entirely possible with cpptraj.
Getting the coordinate/velocity/force data could potentially be done
but it's not straightforward.
I assume the trajectory is in NetCDF format. FYI NetCDF distributions
come with a tool called 'ncdump' which can be used to extract values
from NetCDF files in text format. For example:
ncdump -v coordinates <file>
can be used to extract the coordinates from an Amber NetCDF trajectory
file. 'ncdump -h <file>' can be used to see which variable names are
present in the file.
If you would like this functionality to be a part of cpptraj feel free
to add a feature request to the cpptraj GitHub page:
https://github.com/Amber-MD/cpptraj/issues
-Dan
On Sun, Aug 27, 2017 at 5:41 PM, Jewgeni Starikow
<starikow.tfp.uni-karlsruhe.de> wrote:
> Dear all,
>
>
> I have generated an AMBER trajectory with coordinates, velocities and
> forces at every time point. It is readily readable with the standard
> CPPTRAJ routine.
>
> Now, from this point on, how could I write out the relevant data sets
> in some (text or binary) file readable in some straightforward way?
>
> I would greatly appreciate ordering my corresponding output file like
> as follows:
>
> Atom-Nr Time CoordX CoordY CoordZ VelocX VelocY VelocZ
> ForceX ForceY ForceZ
>
> ... ... ... ... ... ... ... ...
> ... ... ...
>
> ...etc., etc., etc. ...
>
> Which set of the CPPTRAJ commands would be most appropriate for the
> above-outlined case?
>
>
> Respectfully yours,
>
> Evgeni B. Starikov
>
> _______________________________________________
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Aug 28 2017 - 06:00:06 PDT
