Re: [AMBER] Distance calculation between atoms from two different frames using CPPTRAJ

From: Daniel Roe <>
Date: Thu, 4 Jan 2018 09:00:38 -0500

What you want is possible, but only with the GitHub version of cpptraj
(, which allows distance
calculations using a reference frame for the second mask. You want
something like:

parm myparm.parm7
reference 1
distance .1 @1 reference out Atom1.ref.dat

Hope this helps,


On Thu, Jan 4, 2018 at 6:41 AM, anu chandra <> wrote:
> Hello Amber usrs,
> I am trying to calculate distance between two atoms, atomX(f1) and
> atomX(f2-fn). Here 'atomX(f1)' is the atom X from the first frame of the
> trajectory and 'atomX(f2-fn)' is the same atom X, but from the second frame
> to the nth frame. Now I would like to calculate distance between atomX(f1)
> and atomX(f2-fn) along the simulation trajectory. I wonder whether such
> calculation possible with CPPTRAJ. I am aware of 'distance' module in
> CPPTRAJ which calculate the distance between atoms within each frame. Any
> suggestions would be highly appreciated
> Many thanks in advance
> Anu
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Thu Jan 04 2018 - 06:30:03 PST
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