Dear Dan,
thank you for the advice.
I transformed *.mdcrd into *.nc and
did as you told me
trajin combined.nc
trajout forces.nc mdfrc
but unfortunately the forces.nc file is nowhere to see in Amber16 directory.
Cannot help asking why could it not have been written?
Thank you,
Nick
You could potentially use cpptraj. If you just want the forces from a
combined NetCDF file into a NetCDF file containing only forces:
trajin combined.nc
trajout forces.nc mdfrc
If you want them in ASCII format you can write to Amber ASCII
trajectory format by using the forces as coordinates:
trajin combined.nc usefrcascoords:
trajout forces.crd
Hope this helps,
-Dan
On Mon, Apr 9, 2018 at 7:28 AM, Nikolay N. Kuzmich <nnkuzmich.gmail.com>
wrote:
> Dear Amber users and developers,
>
> how is it possible to extract atom forces from the mdcrd file (NetCDF
> format)
> in some structured/ordered manner?
> I tried
> ncdump -v forces name.mdcrd
> and the output goes straight in the terminal window (presumably Fx, Fy,
Fz).
>
> Kind regards,
> Nick
>
> Nikolay Kuzmich
> Department of Drug Safety,
> Research Institute of Influenza,
> WHO National Influenza Centre of Russia,
> 15/17 Professor Popov St.,
> Saint-Petersburg
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Received on Mon Apr 09 2018 - 10:30:03 PDT
