Thank you. I've managed to get it to run the frames I needed.
Sincerely,
Angelina
On Mon, Jun 13, 2016 at 12:37 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> Angelina,
>
> If you are not familiar with cpptraj, please see the tutorial
> http://ambermd.org/tutorials/analysis/#cpptraj
>
> Your command is not correct (I guess due to Dan), should be
>
> *trajin traj.nc <http://traj.nc> 1 1000*
> # where traj.nc is your trajectory filename
>
> cheers
> Hai
>
> On Mon, Jun 13, 2016 at 2:32 PM, Angelina Malagodi <
> angelinamalagodi.gmail.com> wrote:
>
> > Can the syntax be read as is? When I tried I received this error:
> >
> > trajin 1 1000
> >
> > Error: '1': No such file or directory
> >
> > Error: Could not set up input trajectory '1'.
> >
> > On Mon, Jun 13, 2016 at 12:02 PM, Daniel Roe <daniel.r.roe.gmail.com>
> > wrote:
> >
> > > You can specify start and stop frames to the 'trajin' command, e.g.
> > "trajin
> > > 1 1000" to process only the first 1000 frames, etc.
> > >
> > > -Dan
> > >
> > > On Monday, June 13, 2016, Angelina Malagodi <
> angelinamalagodi.gmail.com>
> > > wrote:
> > >
> > > > Okay, but is there a way to compare my first 10 nano seconds to say
> my
> > > last
> > > > 90ns without separating my trajectories into segments?
> > > >
> > > > On Mon, Jun 13, 2016 at 11:44 AM, Daniel Roe <daniel.r.roe.gmail.com
> > > > <javascript:;>> wrote:
> > > >
> > > > > If you processed 1000 frames, the RDF that is output is calculated
> > > > > from all 1000 frames.
> > > > >
> > > > > -Dan
> > > > >
> > > > > On Mon, Jun 13, 2016 at 11:38 AM, Angelina Malagodi
> > > > > <angelinamalagodi.gmail.com <javascript:;>> wrote:
> > > > > > To whom this may concern:
> > > > > >
> > > > > > I have been doing radial distribution functions using a 1000
> frame
> > > > > > trajectory. My results don't indicate if the results are a
> average
> > > over
> > > > > all
> > > > > > of the frames or a single frame. Thank you so much!
> > > > > >
> > > > > > Sincerely,
> > > > > >
> > > > > > Angelina Malagodi
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org <javascript:;>
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> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > -------------------------
> > > > > Daniel R. Roe, PhD
> > > > > Department of Medicinal Chemistry
> > > > > University of Utah
> > > > > 30 South 2000 East, Room 307
> > > > > Salt Lake City, UT 84112-5820
> > > > > http://home.chpc.utah.edu/~cheatham/
> > > > > (801) 587-9652
> > > > > (801) 585-6208 (Fax)
> > > > >
> > > > > _______________________________________________
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> > > > >
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> > > >
> > >
> > >
> > > --
> > > -------------------------
> > > Daniel R. Roe, PhD
> > > Department of Medicinal Chemistry
> > > University of Utah
> > > 30 South 2000 East, Room 307
> > > Salt Lake City, UT 84112-5820
> > > http://home.chpc.utah.edu/~cheatham/
> > > (801) 587-9652
> > > (801) 585-6208 (Fax)
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> > >
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Jun 13 2016 - 12:00:03 PDT
