Dear Daniel,
Thanks for the brief explanation.
An excerpt from AMBER14 manual - page 557 says :
"
*For example, given the dataset {0 1 1 0 1 0 0 0 1 1}, theoverall average
is 0.5. However, there are 3 lifetimes of lengths 2, 1, and 2 (1 1, 1, and
1 1). The max lifetime is 2and the average lifetime is 1.67, i.e. (2 + 1 +
2) / 3 lifetimes = 1.67*."
>From the above lines I think I understand the *Nlifetimes, MaxLT, AvgLT,
TotFrames, SetName*.
By the way, what I am looking for is the lifetime value in pico seconds
(ps).
For example a paper (*Phys. Chem. Chem. Phys.*, 2014, *16.* 324-334)
reports the HB lifetime in ps (Table 3).
Could you explain on how to get the lifetime value in pico second (ps)?
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
> > _______________________________________________
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> > 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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Received on Tue Mar 10 2015 - 20:30:03 PDT
