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
> >> >>> >> 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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>
>
> --
> -------------------------
> 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 Wed Jun 22 2016 - 01:30:09 PDT
