Hi,
You still haven't said whether I was right or wrong about you wanting
to calculate the lifetime of a certain solute atom (or residue) being
involved in *any* hydrogen bond. Since you haven't said no, I will
proceed on the assumption that this is what you want. In that case
this is the procedure I would use.
1) Calculate the hydrogen bond time series data (you have done this).
2) Use a script to sum up all columns involving your atom/residue of
interest. This could be as simple as visually identifying which
columns contain the data you need (e.g. columns 2, 4, 5, and 7) and
using something like awk:
awk '{print $2 + $4 + $5 + $7}' solutehb.dat > sum.dat
3) Read the summed data back into cpptraj with readdata:
readdata sum.dat
4) Perform lifetime analysis on the summed data. The default settings
for cutoff etc will still work since anything greater than 0 means a
hydrogen bond is present:
lifetime sum.dat out life.sum.dat ...
-Dan
On Mon, Mar 16, 2015 at 10:50 AM, Vijay Achari <glycoamber.gmail.com> wrote:
> Dear Dan,
>
> Below is the example you gave to explain on how the calculation of HB can
> done with raw data.
>
>
> 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:
>
>
> Relating to the above example, I understand that we need to add the "1"s
> and divide by total number of lines.
>
> (total of all "1"s) / (total rows with "1"s)
>
>
> So how with the example below? (I modified the above sample).
>
> HB1-1 HB1-2
> 1 0
> 0 1
> 1 0
> 1 1
> 0 1
> 0 0
> 0 0
>
> For the above example is the the average is 6/7 or 6/5. The number 7
> stand for total number of rows and the later stand for rows with the
> presence of "1" (at least once).
>
> Means do I need to count the total rows or the rows with the occurrence of
> "1" only?
>
>
>
> Your explanation would help me to write the script.
>
> Thanks.
>
>
>
> On Thu, Mar 12, 2015 at 4:53 PM, Vijay Achari <glycoamber.gmail.com> wrote:
>
>> Dear Dan,
>>
>> Following your explanation, I would like to verify few things.
>>
>> #1) The file that contains the raw data; is this one "solutehb.dat"
>>
>> if yes,
>>
>> #2) The format of the data in the file is as below?
>>
>> #Frame *BMR_42.O22-BMR_1.O23-H23* BMR_49.O13-BMR_1.O13-H13
>> BMR_59.O13-BMR_2.O22-H22 BMR_10.O13-BMR_2.O26-H26 BMR_61.O26-BMR_3.O22-H22
>> BMR_23.
>> O25-BMR_4.O12-H12 BMR_23.O26-BMR_4.O13-H13 BMR_23.O25-BMR_4.O13-H13
>> BMR_20.O13-BMR_5.O22-H22 BMR_10.O24-BMR_6.O13-H13 BMR_41.O23-BMR_7.O23-H2
>> 3 BMR_41.O24-BMR_7.O23-H23 ....
>>
>>
>> * 1 * 1
>> 1 1 1
>> 1 1 1
>> 1 1 1
>> 1 1 1
>> 1 1 1
>> 1 1 1
>> 1 1
>> 1 1
>> 1 1
>> 1 1
>> 1 1
>> 1 1
>> 1 1
>> 1 1
>> 1 1
>> 1 1
>> 1 1
>> 1 1
>> 1 1 1 . . .
>>
>>
>> #3) So need I operate on this file?
>>
>> #4) Is the first data "BMR_42.O22-BMR_1.O23-H23" is corresponding to the
>> value "1" (below #2)
>>
>> Thank you.
>>
>>
>>
>>
>> On Wed, Mar 11, 2015 at 11:11 PM, Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>>
>>> 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
>>> number of lifetimes is 48, so the average lifetime for BMR_49.O22
>>> 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.
>>> >
>>> > Many thanks in advance.
>>> >
>>> > 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
>>> >>
>>> >> >
>>> >> > Thanks in advance.
>>> >> > 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
>>> >> *solute.lifetime.dat*
>>> >> >> 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
>>> >> hb-lifetime
>>> >> >> 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
>>> >>
>>> > _______________________________________________
>>> > 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)
_______________________________________________
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Received on Sat Mar 21 2015 - 09:30:02 PDT
