Hi,
You will have to use a format that supports both coordinates and
velocities (like NetCDF or Amber restart). If you need the Amber ASCII
trajectory format I will have to add a keyword so that the velocities
will be written in place of the coordinates (making it a "MDVEL"
file). Let me know if you would like this functionality.
-Dan
On Tue, Aug 29, 2017 at 3:31 AM, Pär Håkansson <Nils.Hakansson.oulu.fi> wrote:
> Thanks for the suggestion, however I still have problems
> (I am trying to educate my self on cpptraj, I mainly used some basic ptraj commands before):
> I want to read mdcrd and mdvel files, find the closest solvents and printout the stripped mdcrd and mdvel files
> (or a combined file).
>
> I tired the following (testing with two frames):
> parm Acet_meoh.prmtop
> trajin mdcrd mdvel 1 2 1
> trajout mdcrd
> solvent byres :MOH
> closest 8 :MOL.C1,C2 oxygen closestout closest_meohtest.dat outprefix closesttest
> go
>
> There is no message that velocity files are read and no velocity information in the output so above does not work,
> hence my question is if it is possible to read both mdcrd and mdvel files (or transform them to a NetCDF format)?
>
> Kind regards,
> Pär
>
> ________________________________________
> Från: Daniel Roe <daniel.r.roe.gmail.com>
> Skickat: den 24 augusti 2017 23:00
> Till: AMBER Mailing List
> Ämne: Re: [AMBER] Closest velocities
>
> If the velocities are present in the input trajectory they should be
> present in any output trajectory when 'closest' is used. So you can
> just use 'trajout' to write an output trajectory.
>
> -Dan
>
> On Thu, Aug 24, 2017 at 3:20 PM, Pär Håkansson <Nils.Hakansson.oulu.fi> wrote:
>> Dear Amber list,
>>
>>
>> Using AmberToos16, I have extracted the eight closest solvent molecules to my s?olute "MOL"
>>
>> with the following line in cpptraj script:
>>
>>
>>>closest 8 :MOL.C1,C2 oxygen closestout closest_meoh.dat outprefix closest
>>
>>
>> providing a striped set of coordinates of MOL+8solvents.
>>
>>
>> I have solvent index for each timestep in "closest_meoh.dat", and I could
>>
>> write my own program/script. However,
>>
>> my question is if there is any route to use cpptraj (or other available tools)
>>
>> to extract the corresponding velocities?
>>
>>
>> Kind regards,
>>
>> Pär
>>
>>
>> _______________________________________________
>> 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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> _______________________________________________
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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
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Received on Tue Aug 29 2017 - 12:30:02 PDT
