[gmx-users] HB lifetime

[Erik Marklund]

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> 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
> 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
http://www2.icm.uu.se/molbio/elflab/index.html

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