[gmx-users] HB lifetime

[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
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