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)
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Mar 11 2015 - 00:00:03 PDT
