From: Jason Swails <>
Date: Thu, 05 Dec 2013 08:54:39 -0500

On Thu, 2013-12-05 at 13:32 +0000, John Smith wrote:
> Sorry if I was not so clear. What I meant is atomic fluctuation for which I
> used the following command
> atomicfluct out back.apf .C,CA,N byres
> and I got the dat file. Waht I am trying to do now is to align all the
> frames to the first frame and then calculate the atomic fluctuation. How
> can I do this?

My last email provided the answer. Here it is again:

On Thu, 2013-12-05 at 12:41 +0000, John Smith wrote:
> Hi Amber users
> I am trying to align my trajecotry to get an rmsf using ptraj. I
managed to
> get rmsf but what I could not do is to align the trajectory to the
> frame and then claculate the rmsf

You need to do an RMSD fit first. For example:

rmsd first <mask>
atomicfluct out <filename> <mask>


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Dec 05 2013 - 06:00:03 PST
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