# Re: [AMBER] Evaluating hydrogen boding lifetime

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Tue, 10 Mar 2015 21:50:13 -0600

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

>
> 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:
>> 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
>>
> _______________________________________________
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```--
-------------------------
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
```
Received on Tue Mar 10 2015 - 21:00:02 PDT
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