[gmx-users] H-bond lifetime with g_hbond

[Anna Marabotti]

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.

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.

 

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
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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