Re: [AMBER] Hbond analysis

From: Daniel Roe <>
Date: Wed, 30 Oct 2013 14:36:51 -0600


On Wed, Oct 30, 2013 at 2:31 PM, Fabrício Bracht <> wrote:
> Nevermind the last question. I was thinking about something completely
> different. I guess that the value that really matters is the average for
> the simulation. Right?

I'm not clear on what you mean here. In the lifetime analysis you can
do it over the entire trajectory, or you can look at lifetimes in
separate time windows. If you don't specify 'window' it defaults to
the former (which is equivalent to the lifetime analysis in ptraj's
hbond output). The average over the entire simulation can tell you one
thing, but it can also be instructive to look at smaller time windows
over the entire simulation to see how certain properties evolve.


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 Wed Oct 30 2013 - 14:00:03 PDT
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