AMBER Archive (2005)

Subject: Re: AMBER: Analysing my simulation data..

From: Varsha Goyal (vgusp_at_yahoo.ca)
Date: Sat Jun 18 2005 - 11:21:28 CDT

Dear Vijay,
I guess using VMD would be best idea to calculate RMSD
value. There is tutorial online on AMBER website for
how to use VMD and its well ec\xplained there how to
calculate RMSD.

Vijay Manickam Achari <vjrajamany_at_yahoo.com> wrote:

> Dear Amber users,
>
> I am a novel user of Amber and I have done my
> simulation on micelle strucure in explicit water.
>
> Here I would like to get some advice and guidance
> from
> all the professionals out there the procedure that I
> must follow to get a reliable results of my
> analysis.
>
> I would like to calculate properties like
> RMSD value,
> Radius of Gyration, and
> H-bond for my micelle structure.
>
> In order to calulate the above properties do I need
> to
> reimage the micelle structure?
>
> Is there any other pre-adjustments or pre-setup I
> need
> to do with the output files such as xxxx.mdcrd,
> xxxx.out, xxxx.rst before starting calculation?
>
> I really appreciate your kind advice and guidance.
>
> Thank you
> Vijay.
>
>
>
>
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