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.marabo...@isa.cnr.it <mailto: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)
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
