# Re: [AMBER] Evaluating hydrogen boding lifetime

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 11 Mar 2015 09:11:50 -0600

Hi,

Sorry, it's not clear to me what you're trying to calculate. You said
"I want to know the lifetime of HB for O22 (ACCEPTOR) atom only"; do
you want the average lifetime of any given O22 involved in a hydrogen
bond? In that case you will probably need to write your own script for
it for the time being. I'll try to illustrate why with an example. Say
I want to ask how often is BMR_49.O22 involved in any hydrogen bond as
an acceptor. I could naively sum up the total number of frames the
bond is present (TotFrames) for each instance of this acceptor atom
and then divide by the total number of lifetimes:

4 20 5 1.8500 37
BMR_49.O22-BMR_1.O26-H26
7 28 2 1.0357 29
BMR_49.O22-BMR_1.O13-H13

the total number frames there is a hydrogen bond is 66, and the total
involved in any hydrogen bond (given the data here) is 1.375 frames.
However, this is only true if the data were sequential, because it
doesn't take into account the times when one is present and the other
isn't. For example, given this hydrogen bond data (where HB1
represents a single acceptor):

HB1-1 HB1-2
1 0
0 1
1 0
1 1

Using the method I illustrated before you'd come up with an average of
(5 / 4 = 1.25). However, the actual answer of how often is HB1
involved in a hydrogen bond is clearly all 4 frames, since when HB1-1
is broken, HB1-2 is formed, so its always involved in some kind of
hydrogen bond. So to do what you want you will need to write out the
raw time series data, sum up the columns corresponding to the hydrogen
bonds you are interested in, then run 'lifetime' analysis on that data
set. So using the above sets as an example, the set I would actually
run lifetime analysis on would look like:

(HB1-1)+(HB1-2)
1
1
1
2

Hope this helps,

-Dan

On Wed, Mar 11, 2015 at 12:57 AM, Vijay Achari <glycoamber.gmail.com> wrote:
> Dear Dan,
>
> In my case the time gap in between two frames (taken for analysis) is 5ps.
>
> #Set Nlifetimes MaxLT AvgLT TotFrames SetName
> 0 17 215 55.7059 947
> BMR_42.O22-BMR_1.O23-H23
> 1 1 1 1.0000 1
> BMR_42.O23-BMR_1.O23-H23
> 2 31 3 1.0968 34
> BMR_31.O22-BMR_1.O26-H26
> 3 11 2 1.0909 12
> BMR_31.O13-BMR_1.O26-H26
> 4 20 5 1.8500 37
> BMR_49.O22-BMR_1.O26-H26
> 5 24 4 1.7917 43
> BMR_49.O23-BMR_1.O26-H26
> 6 41 2 1.0488 43
> BMR_49.O12-BMR_1.O12-H12
> 7 28 2 1.0357 29
> BMR_49.O22-BMR_1.O13-H13
> 8 1 1000 1000.0000 1000
> BMR_49.O13-BMR_1.O13-H13
> 9 1 1 1.0000 1
> BMR_22.O12-BMR_2.O22-H22
> 10 50 62 18.9400 947
> BMR_59.O13-BMR_2.O22-H22
> 11 1 1 1.0000 1
> BMR_59.O25-BMR_2.O23-H23
> 12 34 5 1.1471 39
> BMR_59.O13-BMR_2.O23-H23
> 13 7 6 2.1429 15
> BMR_59.O26-BMR_2.O24-H24
> 14 6 8 3.6667 22
> BMR_59.O25-BMR_2.O24-H24
> 15 28 2 1.1071 31
> BMR_10.O26-BMR_2.O26-H26
> 16 52 121 15.1346 787
> BMR_10.O25-BMR_2.O26-H26
> 17 65 9 1.9231 125
> BMR_10.O13-BMR_2.O26-H26
> 18 4 4 2.2500 9
> BMR_59.O26-BMR_2.O26-H26
> 19 9 1 1.0000 9
> BMR_22.O15-BMR_2.O13-H13
> 20 1 1 1.0000 1
> BMR_10.O11-BMR_2.O16-H16
> 21 7 2 1.1429 8
> BMR_53.O13-BMR_2.O16-H16
> 22 2 3 2.5000 5
> BMR_33.O13-BMR_3.O22-H22
> 23 97 54 6.8247 662
> BMR_61.O26-BMR_3.O22-H22
> 24 1 1 1.0000 1
> BMR_29.O26-BMR_3.O23-H23
> 25 31 36 3.3226 103
> BMR_29.O16-BMR_3.O23-H23
> 26 22 2 1.2273 27
> BMR_30.O22-BMR_3.O23-H23
> 27 4 1 1.0000 4
> BMR_33.O22-BMR_3.O23-H23
> 28 38 2 1.1316 43
> BMR_33.O13-BMR_3.O23-H23
> (there are more than 2000 lines, but I work on only 28 lines to get some
> understanding)
>
>
> For clarity, I shall show you how I worked on the given results above.
>
> I want to know the lifetime of HB for O22 (ACCEPTOR) atom only. So, I did
> in this way,
>
> 1) sum the values from column AvgLT for the only occurrences of O22.
> 2) than find the average of that, where the denominator would be the number
> of occurrences of O22.
>
> Based on the above steps, the results are :
>
> O22 occur 6 times,
> sum of O22 is 61.916, and
> average of O22 is 10.319.
>
> So, I figured out the lifetime of O22 would be 10.319 x 5ps = 51.595 ps.
>
> Is this correct? Did I choose the correct column "AvgLT"?
>
> I hope to get some feedback if this is correct way to do it.
>
>
> Vijay
>
>
> On Wed, Mar 11, 2015 at 11:50 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> On Tue, Mar 10, 2015 at 9:24 PM, Vijay Achari <glycoamber.gmail.com>
>> wrote:
>> > Could you explain on how to get the lifetime value in pico second (ps)?
>>
>> This depends on how often you recorded your coordinate trajectory. For
>> example, say you ran a simulation with a timestep of 2 fs (dt=0.002
>> ps) and you recorded a trajectory frame every 500 steps (ntwx=500).
>> This means that each frame in your trajectory has been recorded at 1
>> ps intervals. However, say you recorded your trajectory every 5000
>> steps instead - your trajectory then will have been recorded at 10 ps
>> intervals. Since lifetimes are always given in frames, it should be
>> easy to convert to ps based on how often your coordinate trajectory
>> was written to (e.g. in the latter case a max lifetime of 1 frame
>> would mean 10 ps).
>>
>> Hope this helps,
>>
>> -Dan
>>
>> >
>> > Vijay
>> >
>> >
>> > On Tue, Mar 10, 2015 at 10:15 PM, Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>> >
>> >> Hi,
>> >>
>> >> On Tue, Mar 10, 2015 at 2:53 AM, Vijay Achari <glycoamber.gmail.com>
>> >> wrote:
>> >> > generate two files with lifetime information. The
>> >> contain
>> >> > info like:
>> >> >
>> >> > #Set Nlifetimes MaxLT AvgLT TotFrames SetName
>> >> > 0 22 1 1.0000 22
>> >> BMR_3.O16-BMR_1.O22-H22
>> >> > 1 296 346 15.6959 4646
>> >> BMR_42.O22-BMR_1.O22-H22
>> >> > 2 992 12 1.4688 1457
>> >> BMR_42.O14-BMR_1.O22-H22
>> >> > 3 1 1 1.0000 1
>> >> BMR_42.O13-BMR_1.O22-H22
>> >> > 4 189 12 1.1429 216
>> >> BMR_57.O25-BMR_1.O22-H22
>> >> > 5 462 410 12.3074 5686
>> >> BMR_57.O16-BMR_1.O22-H22
>> >> >
>> >> > I would like to know how I can go from here to calculate the
>> >> between
>> >> > solute and solute?
>> >>
>> >> I'm not really sure I understand your question. The data output you
>> >> posted is exactly the lifetime calculation. For example, the second
>> >> set (1) contains lifetime information for the hydrogen bond between
>> >> residue 42, atom O22 and residue 1, atoms O22-H22; there were 296
>> >> individual lifetimes (i.e. the hbond formed 296 times), the max of
>> >> which lasted 346 frames, the average lifetime is ~15.7 frames. Let me
>> >> know if I'm not understanding you or if I can explain more.
>> >>
>> >> -Dan
>> >>
>> >> >
>> >> > I have read the pages 556-557 from AMBER 14 manual, but I find it
>> >> difficult
>> >> > to see how one should start processing and getting the lifetime value.
>> >> >
>> >> > I think simple example would help me much in this case.
>> >> >
>> >> > Could you give me some example on how this can be obtained?
>> >> >
>> >> > Your help is much appreciated.
>> >> >
>> >> > Thank you.
>> >> > Vijay
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >>
>> >>
>> >> --
>> >> -------------------------
>> >> Daniel R. Roe, PhD
>> >> Department of Medicinal Chemistry
>> >> University of Utah
>> >> 30 South 2000 East, Room 307
>> >> Salt Lake City, UT 84112-5820
>> >> http://home.chpc.utah.edu/~cheatham/
>> >> (801) 587-9652
>> >> (801) 585-6208 (Fax)
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber

```--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Mar 11 2015 - 08:30:02 PDT
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