The trajin command specifies an input trajectory you want to process. So
replace traj.nc with whatever the name of your trajectory file is. See the
manual for complete details of the command. Hope this helps.
-Dan
On Wednesday, March 9, 2016, Vertika Gautam <vartikapisces.gmail.com> wrote:
> Thanks Daniel!
>
> As per your advice now I am calculating correlation matrix. From the
> archives I got this input suggested by you.
>
> *reference average.rst7 *
> *> trajin traj.nc <http://traj.nc> *
> *> rms reference .CA *
> *> matrix correl .CA out matrix_correl_CA.dat *
>
>
> *If you would like the output by residue specify the 'byres' keyword in >
> the 'matrix' command. *
>
> may I know what is traj.nc?
> Please help
>
> Thanks
>
> On Tue, Feb 23, 2016 at 11:57 PM, Daniel Roe <daniel.r.roe.gmail.com
> <javascript:;>> wrote:
>
> > Hi,
> >
> > The velocity autocorrelation function is more for examining the
> > dynamic nature of your system, and is typically used to look at
> > diffusion. Examining if the movement of loops are correlated might be
> > better suited to something like calculation of a dynamic
> > cross-correlation matrix ('matrix correl' in cpptraj). See the manual
> > for further details.
> >
> > Hope this helps,
> >
> > -Dan
> >
> > On Sun, Feb 21, 2016 at 10:27 PM, Vertika Gautam
> > <vartikapisces.gmail.com <javascript:;>> wrote:
> > > Hello everyone,
> > >
> > >
> > > I am trying to use velocity auto correlation function to analyze 3
> loops
> > of
> > > my receptor whether change in their positions during simulation is
> > related
> > > or not?
> > > Does anyone know the script for the same or any help relating to this
> > > matter.
> > >
> > > PS: I am using AMBER12
> > >
> > >
> > >
> > > Thanks in advance
> > >
> > > --
> > > Vertika Gautam
> > >
> > > Research Assistant
> > > Drug Design and Development Research Group (DDDRG)
> > > Department of Chemistry, Faculty of Science
> > > University of Malaya
> > >
> > >
> > >
> > > *e-mail address: vartikapisces.gmail.com <javascript:;>
> > > <vartikapisces.gmail.com <javascript:;>>
> > > vartikapisces.hotmail.com <javascript:;> <vartikapisces.hotmail.com
> <javascript:;>>
> > > 01112294191*
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> Vertika Gautam
>
> Research Assistant
> Drug Design and Development Research Group (DDDRG)
> Department of Chemistry, Faculty of Science
> University of Malaya
>
>
>
> *e-mail address: vartikapisces.gmail.com <javascript:;>
> <vartikapisces.gmail.com <javascript:;>>
> vartikapisces.hotmail.com <javascript:;> <vartikapisces.hotmail.com
> <javascript:;>>
> 01112294191*
> _______________________________________________
> 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)
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 10 2016 - 08:00:06 PST
