Great to hear, thanks for the help!
-Dan
On Saturday, June 25, 2016, SHAILESH KUMAR <shaile27_sit.jnu.ac.in> wrote:
> 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
> <javascript:;>> 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
> <javascript:;>>
> > 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
> <javascript:;>>
> > 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 <javascript:;>
> > >
> > >> 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
> <javascript:;>>
> > >> 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 <javascript:;>>
> > >> >> 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 <javascript:;>
> > >> >> >
> > >> >> > 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
> <javascript:;>>
> > >> 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
> <javascript:;>>
> > >> 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 <javascript:;>>
> > >> >> >>> > 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 <javascript:;>>
> > >> >> 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 <javascript:;>
> > >> >> >>> >> >
> > >> >> >>> >> > 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 <javascript:;>
> > >> >> >>> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >> >>> >> > >
> > >> >> >>> >> > _______________________________________________
> > >> >> >>> >> > AMBER mailing list
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> > >> >> >>> >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >> >>> >> >
> > >> >> >>> >> _______________________________________________
> > >> >> >>> >> AMBER mailing list
> > >> >> >>> >> AMBER.ambermd.org <javascript:;>
> > >> >> >>> >> http://lists.ambermd.org/mailman/listinfo/amber
> > >> >> >>> >>
> > >> >> >>> >
> > >> >> >>> >
> > >> >> >>> _______________________________________________
> > >> >> >>> AMBER mailing list
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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)
> > >> >>
> > >> >> _______________________________________________
> > >> >> AMBER mailing list
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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)
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
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> > >>
> > > _______________________________________________
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> > > AMBER.ambermd.org <javascript:;>
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > -------------------------
> > 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 - 06:00:02 PDT
