From: John Smith <>
Date: Thu, 5 Dec 2013 13:32:12 +0000

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?

Thank you

On 5 December 2013 13:02, David A Case <> wrote:

> On Thu, Dec 05, 2013, John Smith wrote:
> >
> > 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 first
> > frame and then claculate the rmsf
> It's unclear what you mean by "rmsf". But a command like this should work:
> rms first <mask> out rms.dat
> The root-mean-square distance of each frame of the trajectory (relative to
> the
> first frame) will appear in the file "rms.dat".
> ...hope this helps...dac
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Received on Thu Dec 05 2013 - 06:00:02 PST
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