Sarah Witzke wrote:
<snip>
>
> 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.
<snip>
> 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,
Sarah
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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