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)
>
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Mar 12 2015 - 02:00:03 PDT
