Re: [AMBER] about velocity output

From: George Madalin Giambasu <giambasu.gmail.com>
Date: Thu, 18 Nov 2010 08:33:12 -0500

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>>>
> > _______________________________________________
> > 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
>


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Received on Thu Nov 18 2010 - 06:00:06 PST
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