From: David A Case <>
Date: Thu, 5 Dec 2013 08:02:58 -0500

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 - 05:30:04 PST
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