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
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Received on Thu Jun 16 2016 - 11:00:03 PDT
