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 - 10:30:02 PDT
