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From: Vijay Achari <glycoamber.gmail.com>

Date: Thu, 12 Mar 2015 16:53:20 +0800

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

Received on Thu Mar 12 2015 - 02:00:03 PDT

Date: Thu, 12 Mar 2015 16:53:20 +0800

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:

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Thu Mar 12 2015 - 02:00:03 PDT

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