- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Daniel Roe <daniel.r.roe.gmail.com>

Date: Sat, 21 Mar 2015 10:06:20 -0600

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
*

Date: Sat, 21 Mar 2015 10:06:20 -0600

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:

-- ------------------------- 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/amberReceived on Sat Mar 21 2015 - 09:30:02 PDT

Custom Search