[gmx-users] g_hbond

[David van der Spoel]

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.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se