On Sun, Jun 28, 2015 at 5:22 PM, zahra khatti <zkhatti2000.yahoo.com> wrote:
> Dear amber users
> I have run hbond and lifetime analysis in cpptraj using AmberTools14.the
> output look like this:
> #Set Nlifetimes MaxLT AvgLT TotFrames SetName
> 0 2 1 1.0000 2 WAT_178.O-QPT_2
> .N1-H1
> 1 2 1 1.0000 2 WAT_215.O-QPT_2
> .N1-H1
> But I don't about what is the lifetime in ps?please, anyone explain that
> to me.
If you read the discussion about lifetime in the Amber 15 manual (see page
601), the detailed explanation of the examples should help.
Nlifetimes tells you how many "lifetimes" there were. MaxLT tells you the
maximum number of consecutive *frames* in which the data set satisfied your
lifetime cutoff (by default, 0.5 which means an *existing* H-bond counts
and a non-existent H-bond does not).
So what this means is that your average lifetime is 1.0 frames (which seems
to be because your trajectory had two non-adjacent frames with the hydrogen
bond present). The only way you can convert this into ps or ns is to
multiply the number of *frames* in AvgLT by the time between frames in your
trajectory.
For instance, if you set dt=0.002, ntwx=1000, then you are printing out
trajectories every 2 ps. So MaxLT would be 1.0 frames * 2ps/frame = 2 ps.
HTH,
Jason
P.S. An unrelated thing I'll point out is that my Gmail account tries to
send every one of your emails to spam (the only reason it didn't happen is
because of a filter I set up preventing it for Amber emails). This isn't
your fault, but seems to be something that only occurs from Yahoo email
addresses (probably due to some changes in their email policy some time
ago). Since a lot of the developers tend to use Gmail accounts, this may
be preventing your questions from being seen as soon as they otherwise
would be. A possible solution to this would be to register an email
address with another service for interacting with mailing lists (like
Hotmail, Gmail, ... etc.).
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jun 29 2015 - 05:30:04 PDT
