Re: [AMBER] Distance matrix time series

From: Daniel Roe <>
Date: Tue, 3 Jun 2014 08:22:47 -0600


On Mon, Jun 2, 2014 at 4:19 PM, Eugene Yedvabny <> wrote:
> symmetric matrix, as expected. But there doesn't seem to be an explanation
> on whether the values of that matrix are averages across all frames of the
> trajectory or are the distances for only the first/last frame. Is it

The values are the average distance between the given atom pair over all frames.

> possible for cpptraj to generate a 3D matrix where the third dimension is a
> particular frame of the trajectory?

Cpptraj can generate 3D data sets (via the 'hist' command, output
xplor or opendx format), but can't yet e.g. combine a series of 2D
data sets to form a 3D data set, although something like that has been
on my to-do list.

Hope this clears things up,


> I can accomplish that with a cpptraj script full of
> matrix dist .H* out ../analysis/hdist.dat.1 start 1 end 1
> matrix dist .H* out ../analysis/hdist.dat.2 start 2 end 2
> ...
> matrix dist .H* out ../analysis/hdist.dat.N start N end N
> but perhaps there's already a 'neater' way of obtaining the distance time
> series.
> Thank you,
> Eugene Yedvabny
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Jun 03 2014 - 07:30:03 PDT
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