[gmx-users] HB lifetime

Erik Marklund erikm at xray.bmc.uu.se
Thu Mar 29 21:56:49 CEST 2012

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?


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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

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