On Thu, Jan 17, 2013 at 1:53 AM, Vijay Manickam Achari <vjrajamany.yahoo.com
> wrote:
> Dear sir,
>
> I have simulated a box of water molecules using netCDF format
> (using ntwv=-1 in md input file). This generated trajectory files with
> velocity information embedded into traj file. Each trajectory file contain
> 200 frames.
>
> I am trying get restart file with velocity information written into the
> file.
>
> When I tried to use ptraj as below:-
>
> ptraj xx.top << EOF
> trajin aaa.traj 1 5
> trajout bbb.rst restart
> EOF
>
> I get five restart files and when I look into the files the velocities are
> not written into the files. Normally, the restart file contain two parts.
> The top part contain x y z coordinates and the bottom part will contain
> velocities. But the files I generated using above style does not generate
> restart file with coordinates and velocities information.
>
>
> When I scan through Amber manual I could not find description that i want.
>
> Is there any way to get velocity and coordinates written into restart
> files?
>
I wrote a script to do this some time ago, you can find it here --
http://jswails.wikidot.com/helpful-scripts#toc17
In order to use it you will need to install ScientificPython. You can
usually install this package through your package manager (apt-get, yum,
zypper, port, etc.).
HTH,
Jason
--
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 - 07:00:03 PST
