Hi Daniel,
I tested it after fixing and it is fine,
I also tested implementation of mdcrd, mdvel and mdfrc options for trajout
with various one-options two-options and tree-option
combinations with and without strip a subset of atoms, all these are
working as expected.
Thanks
-Shailesh
On Thu, Jun 23, 2016 at 11:00 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I was able to reproduce the problem and I think I have fixed it. Can
> you try the GitHub code again and see if it works for you now? Thanks,
>
> -Dan
>
>
> On Wed, Jun 22, 2016 at 2:00 AM, SHAILESH KUMAR <shaile27_sit.jnu.ac.in>
> wrote:
> > Hi Daniel,
> >
> > I have installed your earlier implementation, and tested it, a am
> > summarising test results.
> >
> > (11) Tests Passed...
> > [('mdfrc.nc', 'CrdFrc.nc'), ('mdfrc.nc', 'CrdVelFrc.nc'), ('mdfrc.nc',
> > 'nosolv_CrdVelFrc.nc'), ('mdfrc.nc', 'strip_CrdVelFrc.nc'),
> ('CrdFrc.nc',
> > 'CrdVelFrc.nc'), ('CrdFrc.nc', 'nosolv_CrdVelFrc.nc'), ('CrdFrc.nc',
> > 'strip_CrdVelFrc.nc'), ('CrdVelFrc.nc', 'nosolv_CrdVelFrc.nc'),
> > ('CrdVelFrc.nc', 'strip_CrdVelFrc.nc'), ('nosolv_CrdVelFrc.nc',
> > 'strip_CrdVelFrc.nc'), ('nosolv-frc_CrdFrc.nc', 'strip_CrdFrc.nc')]
> >
> >
> >
> > (10) Failed Tests...
> > [('mdfrc.nc', 'nosolv-frc_CrdFrc.nc'), ('mdfrc.nc', 'strip_CrdFrc.nc'),
> > ('CrdFrc.nc', 'nosolv-frc_CrdFrc.nc'), ('CrdFrc.nc', 'strip_CrdFrc.nc'),
> > ('CrdVelFrc.nc', 'nosolv-frc_CrdFrc.nc'), ('CrdVelFrc.nc',
> > 'strip_CrdFrc.nc'), ('nosolv_CrdVelFrc.nc', 'nosolv-frc_CrdFrc.nc'),
> > ('nosolv_CrdVelFrc.nc', 'strip_CrdFrc.nc'), ('nosolv-frc_CrdFrc.nc',
> > 'strip_CrdVelFrc.nc'), ('strip_CrdFrc.nc', 'strip_CrdVelFrc.nc')]
> >
> > nosolv prefix is used for trajectories obtained after stripping out
> solvent
> > and ions, while original mdcrd.nc, mdvel.nc & mdfrc.nc were read using
> > trajin
> >
> > strip prefix is used when cpptraj written trajectories were read using
> > trajin
> >
> > It indicates that there is problem in writing Crd+Frc after strip, while
> > Crd+Vel+Frc is fine even after strip.
> >
> > If you say i can share my testdata and script so that you can look into
> it
> > in little detail.
> >
> > On Tue, Jun 21, 2016 at 12:15 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> FYI the 'mdvel', 'mdfrc', and 'mdcrd' options have been implemented
> >> for NetCDF trajectory writes in the GitHub version of cpptraj. See
> >> https://github.com/Amber-MD/cpptraj/pull/359 for details if
> >> interested.
> >>
> >> -Dan
> >>
> >> On Sat, Jun 18, 2016 at 3:44 AM, SHAILESH KUMAR <shaile27_sit.jnu.ac.in
> >
> >> wrote:
> >> > 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
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> >> >> >>> >> >
> >> >> >>> >> _______________________________________________
> >> >> >>> >> AMBER mailing list
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> >> >> >>> >>
> >> >> >>> >
> >> >> >>> >
> >> >> >>> _______________________________________________
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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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> >>
> >>
> >>
> >> --
> >> -------------------------
> >> 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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> >>
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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 25 2016 - 03:00:02 PDT
