[gmx-users] g_hbond

[shahab shariati]

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

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?*
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