[gmx-users] H-bond lifetime with g_hbond

Anna Marabotti anna.marabotti at isa.cnr.it
Tue Oct 11 16:20:15 CEST 2011

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 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
(Roberto Benigni, about Roberto Saviano)
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