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
>> >> >>> >> > AMBER.ambermd.org
>> >> >>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >>> >> >
>> >> >>> >> _______________________________________________
>> >> >>> >> AMBER mailing list
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>> >> >>> >> 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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>>
>>
>>
>> --
>> -------------------------
>> 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 Thu Jun 23 2016 - 11:00:02 PDT
