SV: SV: [gmx-users] Hydrogen bonding

Justin A. Lemkul jalemkul at
Wed Nov 18 23:00:12 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.



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


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