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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu Jun 16 2016 - 10:00:02 PDT
