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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