Here trick is to use force values as coordinate values and load it with the
corresponding prmtop, and write it back as a coordinate trajectory.
Thanks again Hai,
It works.
On Thu, Jun 16, 2016 at 11:22 PM, SHAILESH KUMAR <shaile27_sit.jnu.ac.in>
wrote:
> Thanks Hai,
>
> I am going to try it out and will update about the status.
>
> On Thu, Jun 16, 2016 at 11:11 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
>> So I break my promise to wait. Below is pytraj solution.
>> You need to create a file (e.g myscript.py) then copy my code to your
>> file.
>> then
>>
>> python myscript.py
>>
>> https://github.com/hainm/amber_things/issues/18
>>
>> let me know if that helps.
>>
>> Hai
>>
>> On Thu, Jun 16, 2016 at 1:07 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>>
>> > So you mean loading forces with given parm file and then striping water,
>> > then writing to a new trajectory?
>> >
>> > If yes, I think I can have a solution for you with pytraj.
>> >
>> > But I will wait until Dan or other give you solution with cpptraj first.
>> >
>> > Hai
>> >
>> >
>> > On Thu, Jun 16, 2016 at 12:53 PM, SHAILESH KUMAR <
>> shaile27_sit.jnu.ac.in>
>> > wrote:
>> >
>> >> Thank you for prompt response and suggestion.
>> >>
>> >> I have saved separate coordinate, velocity and force trajectories
>> created
>> >> using below command options with PMEMD.
>> >> -x ${TRAJDIR}/sys.mdcrd.nc \
>> >> -v ${TRAJDIR}/sys.mdvel.nc \
>> >> -frc ${TRAJDIR}/sys.mdfrc.nc
>> >>
>> >> This way I have a coord file, a mdvel file and a force file.
>> >>
>> >> 1. I want to strip out force values from force trajectory as you
>> >> suggested,
>> >> but for that I need to have a trajectory which contains coords as well
>> as
>> >> force values.
>> >>
>> >> 2. "trajout out.nc force" does use of force option asks cpptraj to
>> output
>> >> only force part of the trajectory? or it outputs coords & force?
>> >>
>> >> 3. Is there any way to load only force values not coordinates with the
>> >> corresponding .prmtop file?
>> >> if not then, how to separate coordinated and force trajectory after
>> >> stripping solvents
>> >>
>> >> May be I did not got it right, but I tried to look into source code of
>> >> cpptraj packaged with AmberTools16 and searched for keyword mdfrc and
>> >> found
>> >>
>> >> Trajin_Single.cpp
>> >> 80: // TODO add in support for separate mdfrc file
>> >> 97: // TODO open mdfrc file if present
>> >> 106: // TODO close mdfrc file if present
>> >> 160: // TODO open mdfrc file if present
>> >> 180: // TODO close mdfrc file if present
>> >>
>> >> A similar thread related to mdvel file reading:
>> >> http://archive.ambermd.org/201605/0225.html
>> >>
>> >> suggests use of mdvel keywork with trajin, so I thought that there may
>> be
>> >> mdfrc keyword as well and searched for it in source code, because it
>> was
>> >> mentioned that mdvel option is not documented in manual
>> >>
>> >>
>> >>
>> >> On Thu, Jun 16, 2016 at 8:24 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>> >>
>> >> > do you mean writing coordinates with force?
>> >> >
>> >> > If yes, this is example with *cpptraj*
>> >> >
>> >> > parm systemVF.parm7
>> >> > trajin systemVF.nc
>> >> > strip :WAT
>> >> > trajout out.nc force
>> >> >
>> >> > pytraj does not support that yet.
>> >> >
>> >> > Hai
>> >> >
>> >> > On Thu, Jun 16, 2016 at 9:33 AM, SHAILESH KUMAR <
>> shaile27_sit.jnu.ac.in
>> >> >
>> >> > wrote:
>> >> >
>> >> > > Dear Amber user,
>> >> > >
>> >> > > Are there any ways to read and after striping solvent write out
>> mdfrc
>> >> > > trajectory netcdf files generated by pmemd using cpptraj or
>> pytraj.
>> >> > >
>> >> > > Thank you
>> >> > > _______________________________________________
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>> >> > >
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Received on Thu Jun 16 2016 - 12:00:02 PDT
