Re: [AMBER] Fwd: High RMSD values due to use of iwrap

From: David A Case <>
Date: Wed, 20 Jan 2016 08:06:05 -0500

On Wed, Jan 20, 2016, richa anand wrote:
> I am confused that when I use iwrap why I get high values of RMSD, while
> the same input file to calculate RMSD gives low values of RMSD without
> using iwrap (i.e. iwrap = 0). But using iwrap = 0 simulation get stuck
> after 47.5 ns.
> Please suggest me how to get right values of RMSD. I used 'image' command
> during RMSD calculation.

More details about what you mean when you say "I used image command" would
help; but almost certainly, what you want to use is the "autoimage" command.
This does the "right thing" for most complexes. Also, be sure to visualize
your trajectory (play around with different ways of handling imaging). That
will give you a lot more insight than just plotting RMSD.


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Received on Wed Jan 20 2016 - 05:30:03 PST
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