That is the correct order, yes.
-Dan
On Wed, Apr 11, 2018 at 9:09 AM, Nikolay N. Kuzmich <nnkuzmich.gmail.com> wrote:
> Dear Dan,
>
> eventually I managed to transform the nc file into a text file:
>
> ncdump forces.nc > forces.cdl.
>
> In which order are the forces supposed to be listed there?
>
> [Frame1]
> [atom 1] Fx Fy Fz
> [atom 2] Fx Fy Fz
> ....
> [Frame2]
> [atom 1] Fx Fy Fz
> [atom 2] Fx Fy Fz
> ....
> etc
>
> Am I right?
>
> Thank you,
> Nick
> __________________________
> 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
>>>> ______________________
>>>
>>>
>>> *_________________________ > AMBER mailing list > AMBER.ambermd.org
>>> <http://AMBER.ambermd.org> >
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> <http://lists.ambermd.org/mailman/listinfo/amber> *
>>> _______________________________________________
>>> AMBER mailing list
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>>> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> 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 Thu Apr 12 2018 - 08:30:03 PDT
