On 2011-12-12 07:41, sulatha M. S wrote:
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.
Yes it is DGact.
The DGeq follows from the fraction of COOH that are not forming hydrogen
bonds, option -nhbdist.
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?
This means that the ACF has not equilibrated and you need much longer
sims. You probably got a warning about it.
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
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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