Oops, I meant ~ 104 continuous frames.
________________________________________
From: Krantzman, Kristin D [KrantzmanK.cofc.edu]
Sent: Monday, March 14, 2016 4:34 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Lifetime analysis of backbone hydrogen bonds
Dear Daniel,
This was very helpful!
Therefore, if one residue has 104 frames, this means that the hydrogen bond was present for ~ 104 frames. Just making sure that I understand.
Thanks, Kristin
________________________________________
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Monday, March 14, 2016 3:45 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Lifetime analysis of backbone hydrogen bonds
On Mon, Mar 14, 2016 at 1:28 PM, Krantzman, Kristin D
<KrantzmanK.cofc.edu> wrote:
> I am not sure what the items are in Nlifetime, MaxLT, AvgLT and TotFrames. I
Nlifetime is the total number of lifetimes (i.e. contiguous segments
of time where the hbond was "present") experienced by that hbond.
MaxLT is the maximum lifetime observed in frames.
AvgLT is the average over all lifetimes in frames.
TotFrames is the total number of frames over all lifetimes.
> The second file called crv.backbone.lifetime.dat
> has 26 frames with 60 curves.
> I have read the information in the Amber15 manual, but I am still not understanding exactly what the information means.
A "lifetime curve" is essentially the curve created by adding all
observed lifetimes on top of each other (and normalized so that 0.0 is
1.0 by default). For example, take the raw data set (this could be any
individual *[solutehb] series data):
01111000110000010011110
Each contiguous segment of '1' (i.e. "present") is a lifetime, so for
this set of data 4 lifetimes are observed, with lengths of 4, 2, 1,
and 4. Taken individually they look like:
1111
11
1
1111
The raw "lifetime curve" is then calculated as follows: for each frame
in all lifetimes up to the max lifetime (in this case 4) sum up the
individual lifetimes. So in this case the raw lifetime curve would
look like:
4 3 2 2
You can read this as all four lifetimes are present at frame 1, only
three lifetimes are still present at frame 2, and only two lifetimes
are still present at frames 3 and 4. This gives you information about
the dynamic behavior of the lifetime (is it long-lived, does it decay
quickly, etc).
Hope this helps,
-Dan
> If you have any guidance or suggest a reference that I could read, I would appreciate it.
> Thanks in advance!
> Best, Kristin D. Krantzman
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-------------------------
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Department of Medicinal Chemistry
University of Utah
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Received on Mon Mar 14 2016 - 14:00:04 PDT
