Dear Dan,
thank you, the file forces.nc has been saved.
I would like to ask you and other Amber users for advice
how to obtain the forces values from resulting nc file.
All the best,
Nick
_________________________________________________
Hi,
Were you running cpptraj interactively or via an input script? If
interactively you need to type 'run' or 'go' to initiate trajectory
processing.
-Dan
On Mon, Apr 9, 2018 at 1:09 PM, Nikolay N. Kuzmich <nnkuzmich.gmail.com>
wrote:
> 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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--
-------------------------
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 Tue Apr 10 2018 - 04:00:02 PDT
