AMBER Archive (2009)

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

From: Sally Pias (sallypias_at_gmail.com)
Date: Fri Oct 02 2009 - 14:16:33 CDT

You need to adjust for your timestep when using ptraj to analyze the
RMSD over a trajectory. See TUTORIAL B1: Simulating a small fragment
of DNA, Section 5.2.2 "Analyzing the trajectory":
http://ambermd.org/tutorials/basic/tutorial1/section5.htm

On Fri, Oct 2, 2009 at 1:40 PM, Olotu Odunayo <paxoo_at_nottingham.ac.uk> 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
>
> i get an output, but then the time scale on x-axis didn't come out right?
>
> Two,
>
> has anyone got a sample script on how i can calculate RMSD, to find out how much particular residues have moved.
> thanks
>
>
>
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-- 
Sally C. Pias
Postdoctoral Fellow (CIFellows Project)
Carlos Simmerling Research Group
Stony Brook University
(575) 635-6084 (cell)

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