SV: SV: SV: [gmx-users] Hydrogen bonding
Justin A. Lemkul
jalemkul at vt.edu
Thu Nov 19 02:09:16 CET 2009
Sarah Witzke wrote:
> 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?
I'm not entirely sure. Please see the posts from David in the thread I
referenced before about some potential issues with the ACF in the g_hbond
calculation. I assume you are using version 4.0.x?
> 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]vt.edu | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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