AMBER Archive (2009)

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

From: Olotu Odunayo (paxoo_at_nottingham.ac.uk)
Date: Fri Oct 02 2009 - 12:40:40 CDT

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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