[gmx-users] H-bond lifetime with g_hbond

[Justin A. Lemkul]

Anna Marabotti wrote:
> Dear gmx-users,
> I have a protein with 5 different ligands. For each system I made 30ns 
> simulation and I calculated the lifetime of the H-bonds between protein 
> and ligand with the command:
>  
> g_hbond -f traj.xtc -s topol.tpr -hbm hbmap.xpm -hbn hbond.ndx -ac 
> hbac.xvg -life hblife.xvg
>  
> During all calculations, the printout of the command gave the same warning:
> 
>  
> 
> WARNING: Correlation function is probably not long enough
> 
> because the standard deviation in the tail of C(t) > 0.001
> 
>  
> 
> and as a matter of fact, the tail of C(t) (average C(t) over second half 
> of acf) reported below this warning was always > 0.001, generally 
> comprised between 0.45 and 0.74 with two exceptions: a value of 
> 0.02+/-0.03 and a value of 0.04+/-0.01.
> 

The warning doesn't complain about the value of C(t), it is telling you that the 
standard deviation in the value is unacceptable.

> Therefore, I'm asking if the forward values considered as lifetimes are 
> reliable or not, and in case, what can I do to avoid this warning.
> 

I can't directly comment on this, but it would seems as if the values are not 
adequately converged.

-Justin

>  
> 
> Thank you very much and best regards
> 
> Anna
> 
>  
> ____________________________________________________
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science, CNR
> Via Roma, 64
> 83100 Avellino (Italy)
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> Email: anna.marabotti at isa.cnr.it <mailto:anna.marabotti at isa.cnr.it>
> Skype account: annam1972
> Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
>  
> "When a man with a gun meets a man with a pen, the man with a gun is a 
> dead man"
> (Roberto Benigni, about Roberto Saviano)
>  
> 

-- 
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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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