Since you didn't tell me what command you used to write solutehb.dat,
I'm assuming it was something like this:
hbond H1 series ...
run
writedata solutehb.dat H1[solutehb]
If so, the file solutehb.dat will have 1 + N columns, where N is the
number of solute-solute hydrogen bonds detected. The first column will
be the frame number. The hydrogen bond time series data sets have 1
when a hydrogen bond is present and 0 otherwise.
-Dan
On Thu, Mar 12, 2015 at 2:53 AM, 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 Thu Mar 12 2015 - 09:00:03 PDT
