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*
> _______________________________________________
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> 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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Received on Tue Feb 23 2016 - 08:00:07 PST
