Hi,
On Mon, Jun 2, 2014 at 4:19 PM, Eugene Yedvabny <eyedvabny.berkeley.edu> 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,
-Dan
>
> 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
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Department of Medicinal Chemistry
University of Utah
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Received on Tue Jun 03 2014 - 07:30:03 PDT
