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.marabo...@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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