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> 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> 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>
>> 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
>> >
>> > 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> 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
>> >>> >> > > _______________________________________________
>> >>> >> > > AMBER mailing list
>> >>> >> > > AMBER.ambermd.org
>> >>> >> > > http://lists.ambermd.org/mailman/listinfo/amber
>> >>> >> > >
>> >>> >> > _______________________________________________
>> >>> >> > AMBER mailing list
>> >>> >> > AMBER.ambermd.org
>> >>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >>> >> >
>> >>> >> _______________________________________________
>> >>> >> AMBER mailing list
>> >>> >> AMBER.ambermd.org
>> >>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>> >>
>> >>> >
>> >>> >
>> >>> _______________________________________________
>> >>> AMBER mailing list
>> >>> AMBER.ambermd.org
>> >>> http://lists.ambermd.org/mailman/listinfo/amber
>> >>>
>> >>
>> >>
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > 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
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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 Mon Jun 20 2016 - 12:00:05 PDT
