Dear all,
I'm trying to find the hydrogen bonding lifetime between a solute and its
surrounding solvent molecules. I have followed a similar procedure as in
the tutorial (
http://www.amber.utah.edu/AMBER-workshop/London-2015/Hbond/)
and read the explanation in the thread (
http://archive.ambermd.org/201603/0280.html) which made the calculation
pretty much clear. According to the thread the lifetime curve consists with
integer numbers like 4 3 2 2 and so on.
1) However, I still can't understand how the lifetime curve obtained in the
tutorial is in fraction and decaying from 1 to 0. Based on that, what is
the basic calculation to generate the lifetime curve form hydrogen bonding
time-series data?
2) In my analysis, am getting the HB time-series data for 193 bonds. But,
by using the 'lifetime' attribute in cpptraj I get only 'curve0' with all
values 1 for all 1000 frames. I have reduced the cutoff to min 0.1. Even
then I am getting only the Curve0. Any suggestion to troubleshot the issue?
Best Reagards,
Bharat Manna
PhD Scholar
IIT Kharagpur
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Received on Wed Aug 22 2018 - 23:00:03 PDT
