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>>
> _______________________________________________
> 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
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Received on Wed Nov 17 2010 - 16:30:06 PST
