[AMBER] Distance matrix time series

From: Eugene Yedvabny <eyedvabny.berkeley.edu>
Date: Mon, 2 Jun 2014 15:19:35 -0700

Hello Amber Community,

I am trying to understand the behavior of the 'matrix dist' command when
applied on a entire trajectory. In particular, I am using the following
command to output the inter-hydrogen distances for the entire protein
(solvent has already been stripped out):

matrix dist .H* out hdist.dat

There are 325 hydrogens in the protein, so hdist.dat is a 325 * 325
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
possible for cpptraj to generate a 3D matrix where the third dimension is a
particular frame of the trajectory?

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

Thank you,
Eugene Yedvabny
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Received on Mon Jun 02 2014 - 15:30:03 PDT
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