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> 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> 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
> > <vartikapisces.gmail.com>
> > vartikapisces.hotmail.com <vartikapisces.hotmail.com>
> > 01112294191*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > 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
>
--
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
<vartikapisces.gmail.com>
vartikapisces.hotmail.com <vartikapisces.hotmail.com>
01112294191*
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Received on Wed Mar 09 2016 - 21:30:03 PST
