Hi George:
Thank you. I will try it.
Best wishes
Hongbin
On Thu, Nov 18, 2010 at 5:33 AM, George Madalin Giambasu <giambasu.gmail.com
> wrote:
> Hi,
>
> attached is a raw python script that can extract the coordinates and
> velocities from a netcdf trajectory and output the rst file to the standard
> output.
> Set the "frame" variable (line 4) to the frame you want to extract, and the
> "inputfile" variable (line 5) to the name of the netcdf trajectory file.
>
> Let us know if it works,
>
>
> George
>
>
>
>
> On Wed, Nov 17, 2010 at 7:28 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > Hi,
> >
> > A colleague of mine has informed me that I'm in fact quite wrong here.
> He
> > has a script that will do this. Basically, what you need is some kind of
> > interface to netcdf-encoded files. Python has a module that interfaces
> to
> > it (see the netcdf website). Then you can create a script to do this for
> > you, or perhaps he will respond to this post.
> > http://www.unidata.ucar.edu/software/netcdf/software.html#Python is the
> > website, and apparently this package is available through
> > "ScientificPython".
> >
> > Hope this helps,
> > Jason
> >
> > On Wed, Nov 17, 2010 at 6:06 PM, hong-bin Xie <xhbxhb1980224.gmail.com
> > >wrote:
> >
> > > Hi Jason:
> > >
> > > Thank you.
> > > I used ptraj to do this. However, it does not work. The following are
> > > commands I used. Please correct me if anything is wrong.
> > > trajin mdvel
> > > trajout velocity
> > >
> > > mdvel is binary format of velocity.
> > >
> > > Best wishes
> > > Hongbin
> > >
> > > On Wed, Nov 17, 2010 at 3:21 PM, Jason Swails <jason.swails.gmail.com
> > > >wrote:
> > >
> > > > Hello,
> > > >
> > > > On Wed, Nov 17, 2010 at 5:59 PM, hong-bin Xie <
> xhbxhb1980224.gmail.com
> > > > >wrote:
> > > >
> > > > > Hi amber users:
> > > > >
> > > > > I want to save velocity sets in the amber MD simulation. The
> keyword
> > > > "ntwv"
> > > > > was used.
> > > > > However, amber 10 version can just save the velocity sets with
> binary
> > > > > NetCDF
> > > > > trajectory. I want to know how to change binary NetCDF format to
> > normal
> > > > > format.
> > > > >
> > > >
> > > > You can probably get ptraj to do this. See if it works properly just
> > > > treating it like a coordinate trajectory file, since it should be
> > largely
> > > > the same (except instead of x,y,z coords, it's x,y,z velocities).
> > Others
> > > > may correct me here if I'm wrong.
> > > >
> > > > Good luck!
> > > > Jason
> > > >
> > > >
> > > > >
> > > > > Any help could be greatly appreciated.
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Jason M. Swails
> > > > Quantum Theory Project,
> > > > University of Florida
> > > > Ph.D. Graduate Student
> > > > 352-392-4032
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Best Wishes
> > > Sincerely Yours
> > > Hong-bin Xie
> > > ---------------------------------------------------------------
> > > Hong-bin Xie
> > > Postdoctoral Researcher
> > > Department of Chemistry
> > > University of California at Irvine
> > > Email:xhbxhb1980224.gmail.com <Email%3Axhbxhb1980224.gmail.com> <
> Email%3Axhbxhb1980224.gmail.com <Email%253Axhbxhb1980224.gmail.com>> <
> > Email%3Axhbxhb1980224.gmail.com <Email%253Axhbxhb1980224.gmail.com> <
> Email%253Axhbxhb1980224.gmail.com <Email%25253Axhbxhb1980224.gmail.com>>>
> <
> > > Email%3Axhbxhb1980224.gmail.com <Email%253Axhbxhb1980224.gmail.com> <
> Email%253Axhbxhb1980224.gmail.com <Email%25253Axhbxhb1980224.gmail.com>> <
> > Email%253Axhbxhb1980224.gmail.com <Email%25253Axhbxhb1980224.gmail.com><
> Email%25253Axhbxhb1980224.gmail.com<Email%2525253Axhbxhb1980224.gmail.com>
> >>>
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > 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
>
>
--
Best Wishes
Sincerely Yours
Hong-bin Xie
---------------------------------------------------------------
Hong-bin Xie
Postdoctoral Researcher
Department of Chemistry
University of California at Irvine
Email:xhbxhb1980224.gmail.com <Email%3Axhbxhb1980224.gmail.com>
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Received on Thu Nov 18 2010 - 11:00:03 PST
