SV: SV: [gmx-users] Hydrogen bonding

Sarah Witzke sawit02 at
Wed Nov 18 22:49:13 CET 2009

Sarah Witzke wrote:


> Yes, I see this. Do you by the way know why this .ndx files under the title [ donors_hydrogens_DMPC ] lists a lot of  non-heteroatoms (carbon atoms)?

No clue.  Probably the code identifies the functional group to which the donor
belongs.  The more pertinent directive is the [ hbonds... ] one, which contains
the indices of the atoms actually participating in hydrogen bonding.


> When I use the -ac option I get this output:
> ...
>   ACF 53/53
>   Normalization for c(t) = 1.19876 for gh(t) = 9.96115e-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): 0.0155651 +/- 0.014574
>   Hydrogen bond thermodynamics at T = 298.15 K
>   Fitting parameters chi^2 = 5.76828e-05
>   Q =          0
>   --------------------------------------------------
>   Type      Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
>   Forward         0.001    682.571      20.705  5.76828e-05
>   Backward        0.013     75.432      15.245
>   One-way         0.001   1001.338      21.655
>   Integral        0.000   3419.839      24.700
>   Relaxation      0.001   1216.745      22.138
>   100%
> ...
> When looking at the produced .xvg file I see these three data sets as a function of time:
>   @ s0 legend "Ac\sfin sys\v{}\z{}(t)"
>   @ s1 legend "Ac(t)"
>   @ s2 legend "Cc\scontact,hb\v{}\z{}(t)"
>   @ s3 legend "-dAc\sfs\v{}\z{}/dt"
> In neither the output nor the .xvg file I see any mention of 'Forward lifetime'. Perhabs this is because of the warning 'Correlation function is probably not long enough because the standard deviation in the tail of C(t) > 0.001' which I sadly don't understand. Is this a matter of actual length of the .xtc file? I use the last 120 ns of a 220 ns simulation. Any suggestions?

Please see the following output line:

Forward         0.001    682.571      20.705  5.76828e-05
ARRGH, I'm sorry, things went too quick :-( So the lifetime in average per hbond is 628.571 ps?

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?

Thank you,




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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