Hi,
If you getting the forces in an ASCII format, you can try:
trajin combined.nc usefrcascoords
trajout forces.crd
go
This will print the forces to 'forces.crd' in Amber ASCII trajectory
format which is relatively simple to parse and is described here:
http://ambermd.org/formats.html#trajectory
-Dan
On Tue, Apr 10, 2018 at 6:41 AM, Nikolay N. Kuzmich <nnkuzmich.gmail.com> wrote:
> 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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>> <http://AMBER.ambermd.org> >
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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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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
https://www.lobos.nih.gov/lcb
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Received on Tue Apr 10 2018 - 06:30:03 PDT
