Re: AMBER: correlation

From: David A. Case <>
Date: Mon, 28 Feb 2005 09:32:54 -0800

On Thu, Feb 24, 2005, Gustavo Pierdominici Sottile wrote:

> When using the correlation option in ptraj I do
> not understand what do tstep, tcorr and tmax mean. tstep is allways set to
> 1, the second one determines the number of lines that are output and it may
> be the number configurations that are taken in account, but related to the
> third one I have no idea. Both the second are the third must be smaller that
> the number of configuration.

I assume(?) you are using Amber 7. "tstep" is supposed to be the time between
snapshots in the trajectory, but in fact (I think) is set to one. This means
that you have to convert "snapshot number" to "time" yourself.

"tcorr" is the maximum time to which the correlation functions will be
computed. Generally, correlation functions evaluated at times more than
about 1/4 of the total simulation time are less statistically reliable.

"tmax" is the stopping point for evaluating the trajectory, even if the
trajectory you give it is longer than this. This is generally not a very
useful parameter, but you could use it (say) to compute what the result would
be for the first half of your trajectory, and compare that to the results of
the total trajectory.

> In the output each line has the colums, what do they mean? x y and z. If so
> I have values greater than one that sounds rare

Can you post a piece of the output that you don't understand?


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Received on Mon Feb 28 2005 - 17:53:01 PST
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