Hi,
Thanks for the report. I'll look into it ASAP.
-Dan
On Wednesday, June 22, 2016, 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
> <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
> > >> >>> >> > AMBER.ambermd.org <javascript:;>
> > >> >>> >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >>> >> >
> > >> >>> >> _______________________________________________
> > >> >>> >> AMBER mailing list
> > >> >>> >> AMBER.ambermd.org <javascript:;>
> > >> >>> >> http://lists.ambermd.org/mailman/listinfo/amber
> > >> >>> >>
> > >> >>> >
> > >> >>> >
> > >> >>> _______________________________________________
> > >> >>> AMBER mailing list
> > >> >>> AMBER.ambermd.org <javascript:;>
> > >> >>> http://lists.ambermd.org/mailman/listinfo/amber
> > >> >>>
> > >> >>
> > >> >>
> > >> > _______________________________________________
> > >> > AMBER mailing list
> > >> > 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)
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org <javascript:;>
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > > _______________________________________________
> > > AMBER mailing list
> > > 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)
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> 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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 22 2016 - 05:00:02 PDT
