ptraj ignores velocities, to the best of my knowledge. You need to use the
script I sent you in the last thread in order to get restart files with
velocities.
HTH,
Jason
On Thu, Jan 17, 2013 at 8:43 AM, Vijay Manickam Achari <vjrajamany.yahoo.com
> wrote:
> Dear experts,
>
> I used vtwv=-1 in order to have velocity information in my trajectory file
> in my md input file.
> Once finish with simulation I wanted to select frames from trajectory
> files.
>
> I did as below:
>
> ptraj abc.top << EOF
> trajin ../traj-waters/waters1445-MD001-run01.traj 1 200 10
>
> trajin ../traj-waters/waters1445-MD001-run02.traj 1 200 10
> unwrap :1-1445
> center :1-1445
> trajout md-water.center.reimage.set01.traj cdf
> EOF
>
>
> Once finish I tried to use script as in
> http://jswails.wikidot.com/helpful-scripts#toc17, suggested by Jason to
> extract velocities, but I get all zero values.
>
> If I extract velocities using trajectories before selecting I do get the
> values for velocity.
>
> What is the could be to incorporate the velocities into the selected
> trajectories as well?
>
> Regards
>
> Vijay
>
>
> Vijay Manickam Achari
> (Phd Student c/o Prof Rauzah Hashim)
> Chemistry Department,
> University of Malaya,
> Malaysia
> vjramana.gmail.com
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jan 17 2013 - 07:00:04 PST
