Re: [AMBER] Calculate average property

From: Jason Swails <>
Date: Tue, 17 Sep 2013 10:24:16 -0400

On Tue, Sep 17, 2013 at 7:05 AM, Gargi Borgohai <>wrote:

> Dear amber Users,
> I want to calculate average value of 'folded fraction' (at a particular
> temperature) of a protein which is simulated by REMD method. For this
> purpose temperature based trajectories are generated first. After that is
> it necessary to take average over all the frames at that particular
> temperature?

As opposed to what alternative? I'm a bit confused here. If you want the
"fraction folded", then you need to come up with some metric for deciding
whether a protein is 'folded' or not, and you count up the number of
snapshots that are 'folded' and divide that by the total number of
snapshots you are considering.

Some people consider all snapshots; others omit some for one reason or
another -- it all depends on what questions you want to ask or what you're
hoping to learn.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Sep 17 2013 - 07:30:03 PDT
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