[gmx-users] g_hbond

[sulatha M. S]

Dear David,

Yes it is DGact.
> The DGeq follows from the fraction of COOH that are not forming hydrogen
> bonds, option -nhbdist.


So, I need to use the equation (9) and (10) from your paper to calculate
the equilibrium constant and 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?
>>
> This means that the ACF has not equilibrated and you need much longer
> sims. You probably got a warning about it.


I did not get a warning here. I also have simulations (20ns) of copolyacids
where again it gave me negative life time. These runs are well equilibrated
with respect to energy and Rg of the polymers. The system is a 20 repeat
unit chain in approx. 5500 water molecules. I have done simulations in
which 10 units are COO- and the remaining 10 as COOH along the chain. With
a 10ns trajectory, the average life time of H-bonds is positive.Only in the
case of unionized acid I am getting a negative life time.


> 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
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What is the value for free energy of H-bonding.
>
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