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:;>
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > >
> > > >
> > > > --
> > > > -------------------------
> > > > 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)
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org <javascript:;>
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org <javascript:;>
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > -------------------------
> > 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)
> > _______________________________________________
> > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 13 2016 - 12:00:02 PDT
