Good suggestions! I'll probably implement those soon.
-Dan
On Saturday, June 18, 2016, 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
> <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
> > >>> >> > >
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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
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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 18 2016 - 07:30:02 PDT
