Hi Jason:
Thank you. I am just wondering whether your colleague would like to share
his script with me.
Best wishes
Hongbin
On Wed, Nov 17, 2010 at 4:28 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>>>
> > _______________________________________________
> > 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>
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Received on Wed Nov 17 2010 - 17:00:03 PST
