[gmx-users] g_hbond

[sulatha M. S]

Dear gromacs users,

I did a g_hbond -ac analysis on a 10 ns trajectory of a polycarboxylate in
water. Following is the output I obtained for the polycarboxylate H-bondign
with water

ACF 36008/36008
Normalization for c(t) = 0.00709164 for gh(t) = 7.09124e-07
Hydrogen bond thermodynamics at T = 298.15 K
Fitting parameters chi^2 = 0.000661899
Q =          0
--------------------------------------------------
Type      Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
Forward         0.300      3.334       7.513  0.000661899
Backward        1.608      0.622       3.350
One-way         0.089     11.284      10.536
Integral        0.039     25.374      12.544
Relaxation      0.062     16.080      11.413

I have read David paper (2006) on thermodynamics of H-bonding. In the paper
two delta G values are mentioned. one is the Gibbs energy of activation
(dG#) and another is the free energy of H-bonding. In the output given from
the -ac analysis, which dG values do these correspond to? I assumed dG
given for the forward rate correspond to the energy of activation. Is it
correct? What is the value for free energy of H-bonding.

Another question I have is, for a polycarboxylic acid system in water (COOH
groups as side chains) for a 10ns run, I got the following as the output
where the life time of the H-bond (between the polyacid and water) is
negative. Is this correct?

ACF 22057/22057
Normalization for c(t) = 0.0217714 for gh(t) = 4.35398e-06
Hydrogen bond thermodynamics at T = 298.15 K
Fitting parameters chi^2 =  0.0146697
Q =          0
--------------------------------------------------
Type      Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
Forward        -0.271     -3.687    -666.000   0.0146697
Backward       -2.291     -0.437    -666.000
One-way         0.101      9.882      10.207
Integral        0.034     29.376      12.907
Relaxation      0.063     15.803      11.370


Thankyou for any help,

Dr. M. S. Sulatha
Dept. of Chemical Engineering
IIT-Madras
India
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