Thanks Danial,
I am grateful to you for adding this feature.
I would try it out for sure and will update about it.
In my opinion if some time in future it can be done
adding mdvel and mdfrc options with trajout will give user more control
over his output need.
for example if we give trajout command as below to attain different things
trajout CrdFrcVel.nc
or
trajout mdcrd mdvel mdfrc CrdFrcVel.nc
# to get combined trajectory containing coords, vels and frcs
trajout mdvel Vel.nc
# to get trajectory containing only velocities
trajout mdfrc Frc.nc
# to get trajectory containing only forces
trajout mdcrd Crd.nc
# to get trajectory containing only coordinates
and similarly two of options {mdcrd, mdvel, mdfrc}
eg.
trajout mdcrd mdfrc CrdFrc.nc
trajout mdcrd mdvel CrdVel.nc
trajout mdvel mdfrc VelFrc.nc
to get output trajectory containing two sets in output trajectory
On Sat, Jun 18, 2016 at 1:14 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> >>> >> > > _______________________________________________
> >>> >> > > 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
> >>> >> >
> >>> >> _______________________________________________
> >>> >> AMBER mailing list
> >>> >> AMBER.ambermd.org
> >>> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>> >>
> >>> >
> >>> >
> >>> _______________________________________________
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> >>>
> >>
> >>
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>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Sat Jun 18 2016 - 03:00:02 PDT
