SV: SV: SV: [gmx-users] Hydrogen bonding

Sarah Witzke sawit02 at
Wed Nov 18 23:53:19 CET 2009


Sarah Witzke wrote:


> ARRGH, I'm sorry, things went too quick :-( So the lifetime in average per hbond is 628.571 ps?

Yes, per the calculation.  For a bit more about the analysis, see the "Please
read and cite" notices, as well as this thread:

> The note about the correlation function would imply that the correlation
> function itself has not converged until its value is < 0.001.  This is usually a
> result of insufficient data, either the length of the simulation, or number of
> frames analyzed (based on the spacing of the frames).
> Hmm, so using 120 ns simulation from a standard .xtc file (timestep of 10 ps) is not long enough. Perhabs I should try the original .trr file... The .xtc file I'm using only contains DMPC and the small molecule, no solvent - I can't see this would make a difference in this case, am I right?

The correlation will depend on how much the interactions are changing over the
period you analyzed.  If you are analyzing a small molecule and DMPC, water
should not matter.

I have now tried with the full length (220 ns) .trr file and the -ac output still prints a warning:

  ACF 106/106
  Normalization for c(t) = 1.23261 for gh(t) = 5.58815e-05

  WARNING: Correlation function is probably not long enough
  because the standard deviation in the tail of C(t) > 0.001
  Tail value (average C(t) over second half of acf): 0.000172327 +/- 0.00277407

In your opinion, does this mean that I cannot trust the value of the lifetime, since the correlation function is not converging?

Thank you!

I have conducted the analysis on the 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at] | (540) 231-9080

gmx-users mailing list    gmx-users at
Please search the archive at before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at
Can't post? Read

More information about the gromacs.org_gmx-users mailing list