[gmx-users] HB lifetime

[Justin A. Lemkul]

Nidhi Katyal wrote:
> yes  acf  14477/14477 .

I believe what Erik has been asking is if you have plotted the ACF curve that 
g_hbond produces to see if there is any anomalous behavior.

> But rmsd plot did give indication about the convergence.

What RMSD plot?

-Justin

> Thank you in advance.
> 
> On Fri, Mar 30, 2012 at 4:26 AM, Erik Marklund <erikm at xray.bmc.uu.se 
> <mailto:erikm at xray.bmc.uu.se>> wrote:
> 
>     Ah. -666 is used whenever the sitting of the kinetic model fails to
>     converge. This is a poor way of signalling that something went wrong
>     that should be changed. Again, did you *look* at the acf?
> 
>     Erik
> 
>     30 mar 2012 kl. 11.53 skrev Nidhi Katyal:
> 
>>     for another system (at 250K) also i have calculated hydrogen bond
>>     lifetime using:
>>     hbond -f *.xtc -s *.tpr -ac *.xvg -num *.xvg -life *.xvg -temp 250
>>      whose output is :
>>     acf  14477/14477
>>     normalization for c(t)=0.0135742 for gh(t)=6.78702e-05 
>>     hydogen bond thermodynamics at T=250K
>>     fitting parameters chi^2 = 3.89447e-06
>>     Type          rate       time      DG          chi^2
>>     forward      -1.201   -0.833   -666.000   3.89447e-06
>>     backward   -0.354   -2.823   -666.000   
>>     ......
>>
>>     Here again i am getting negative hydrogen bond lifetime.
>>     Please suggest me where i am getting wrong and what does negative
>>     lifetime mean?
>>     Thank you in advance.
>>
>>
>>     On Thu, Mar 29, 2012 at 12:56 PM, Erik Marklund
>>     <erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>> wrote:
>>
>>
>>         29 mar 2012 kl. 18.47 skrev Nidhi Katyal:
>>
>>>         Dear All
>>>         I would like to know the strength of the given bond by
>>>         calculating the lifetime of that bond.For the same reason i used:
>>>         g_hbond -f *.xtc -s *.tpr -ac *.xvg -temp 300 -num *.xvg
>>>         -life *.xvg
>>>         and i got:
>>>         Type        Rate(1/ps)  Time(ps)  ...
>>>         Forward    -0.182        -5.495
>>>         .......
>>>         HB lifetime=50.60ps
>>>         Note that the lifetime obtained in this manner is close to
>>>         useless.Use the -ac option instead and check the forward
>>>         lifetime.
>>>         ..
>>>         Will it be correct to say that lifetime is -5.495ps (looking
>>>         at forward time)? But then what does negative lifetime implies?
>>>         Thanks in advance.
>>
>>         Seems weird. Could the amount of underlying data be
>>         insufficient? Have you looked at the acf?
>>
>>         Erik
>>
>>>         -- 
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>>
>>         -----------------------------------------------
>>         Erik Marklund, PhD
>>         Dept. of Cell and Molecular Biology, Uppsala University.
>>         Husargatan 3, Box 596,    75124 Uppsala, Sweden
>>         phone:    +46 18 471 6688        fax: +46 18 511 755
>>         erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>
>>         http://www2.icm.uu.se/molbio/elflab/index.html
>>
>>
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> 
>     -----------------------------------------------
>     Erik Marklund, PhD
>     Dept. of Cell and Molecular Biology, Uppsala University.
>     Husargatan 3, Box 596,    75124 Uppsala, Sweden
>     phone:    +46 18 471 6688        fax: +46 18 511 755
>     erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>
>     http://www2.icm.uu.se/molbio/elflab/index.html
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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