[gmx-users] g_hbond

[David van der Spoel]

On 2010-03-13 09.40, shahab shariati wrote:
> I used g_hbond for analysis of hydrogen bonds.
>
> g_hbond -f *.xtc -s *.tpr -n *.ndx -num -g -ac -dist -ang -hx -hbn -hbm
> -don -dan -life -nhbdist -a 30 -r 0.35
>
> Following text was turned up:
>
> ACF 288/288
>
> Normalization for c(t) = 0.0204067 for gh(t) = 8.10294e-06
>
> 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): 0.685894 +/- 0.00448515

You should do a *much* longer simulation. Since the forward rate for 
breaking is 65 ps you should do at least 10-20 ns.


>
> Hydrogen bond thermodynamics at T = 298.15 K
>
> Fitting parameters chi^2 = 0.0199698
>
> Q = 0
>
> --------------------------------------------------
>
> Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2
>
> Forward 0.015 65.068 14.879 0.0199698
>
> Backward 0.009 108.405 16.144
>
> One-way 0.020 48.818 14.166
>
> Integral 0.007 143.963 16.847
>
> Relaxation 0.085 11.787 10.644
>
> HB lifetime = 10.98 ps
>
> Note that the lifetime obtained in this manner is close to useless
>
> Use the -ac option instead and check the Forward lifetime
>
> *Is my manner wrong? *
>
> * *
>
> *What  job Should be done?*
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se