Hi,
It seems Hai may have gotten you what you needed, but in case you are
interested I have implemented the 'mdfrc' option for 'trajin' in
cpptraj from the GitHub repo: https://github.com/Amber-MD/cpptraj
Usage would be something like:
parm ../tz2.nhe.parm7
trajin short.crd mdvel short.vel mdfrc short.frc
trajout CrdFrcVel.nc
If you do get a chance to try it out I would appreciate any feedback.
Thanks for the report.
-Dan
On Thu, Jun 16, 2016 at 12:56 PM, SHAILESH KUMAR <shaile27_sit.jnu.ac.in> wrote:
> 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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>>> >> > > AMBER.ambermd.org
>>> >> > > http://lists.ambermd.org/mailman/listinfo/amber
>>> >> > >
>>> >> > _______________________________________________
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>>> >> >
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>>> >
>>> >
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>>
>>
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--
-------------------------
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Department of Medicinal Chemistry
University of Utah
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Received on Fri Jun 17 2016 - 13:00:05 PDT
