Re: [AMBER] difference between %occupied and lifetime in hydrogen bond analysis

From: Daniel Roe <>
Date: Thu, 15 Dec 2016 11:18:01 -0500

Since you mentioned '%occupied' I assume you're using 'hbond' from
ptraj. Consider using 'hbond' from cpptraj in the future, which is
easier to use (in my opinion) and has additional features such as
automatic exclusion of intramolecular hydrogen bonds and
distance/angle imaging. The syntax is different though (prior
'acceptor' and 'donor' keywords are not required for example) so be
sure to check the Amber 16 manual.

On Thu, Dec 15, 2016 at 3:17 AM, Andrew Bostick
<> wrote:
> What is the difference between %occupied and lifetime in hydrogen bond
> analysis in amber.

The '%occupied' is just how many frames the hydrogen bond is
considered formed over the total number of frames times 100. The
lifetime statistics get into more detail the behavior of the hydrogen
bond itself. The manual entry for the 'lifetime' analysis command in
cpptraj has a good explanation of this:

"A “lifetime” is defined as the length of time something remains
’present’; data is considered present when above or below a certain
cutoff (the default is greater than 0.5, useful for analysis of hbond
time series data). For example, in the case of a hydrogen bond
’series’ data set, if a hydrogen bond is present during a frame the
value is 1, otherwise it is 0. Given the hbond time series data set {1
1 1 0 1 0 0 0 1 1}, the overall fraction present is 0.6. However,
there are 3 lifetimes of lengths 3, 1, and 2 ({1 1 1}, {1}, and {1
1}). The maximum lifetime is 3 and the average lifetime is 2.0, i.e.
(3 + 1 + 2) / 3 lifetimes = 2.0."

Hope this helps,


> The more %occupancy, the more lifetime?
> Is there the direct relation between them?
> _______________________________________________
> 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 Dec 15 2016 - 08:30:02 PST
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