AMBER Archive (2009)

Subject: Re: [AMBER] RMSD vs time and RMSD vs residues

From: case (case_at_biomaps.rutgers.edu)
Date: Fri Oct 02 2009 - 14:12:23 CDT

On Fri, Oct 02, 2009, Olotu Odunayo wrote:
>
> Hi I was wondering if anyone knows how to calculate RMSD vs time in
> AMBER 10, if you have written your trajectory files (ntwx) in number of
> different steps e.g

> ntwx=50 and
> ntwx=100
>
> I have used
> trajin xx.mdcrd 1 2
> trajin dd.mdcrd
> rms first mass out filename.rms :1-270

You need three numbers (not two) in the first trajin command. For example

trajin xx.mdcrd 2 1000 2 # if xx.mdcrd has 1000 frames with ntwx=50
trajin dd.mdrd # if dd.mdcrd has a arbitrary number of frames
                            # with ntwx=100

This will give you every 2nd frame of the first file (corresponding to every
100th time step), and every frame of the second file (also corresponding to
every 100th time step).

Hope this helps....dac

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