[gmx-users] g_hbond

[David van der Spoel]

On 2011-12-12 09:54, sulatha M. S wrote:
> 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.
Yes.

>
>
>         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.
>
Did you look at the ACF graph? It could be constant at 1 or 0.
>
>     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 <mailto:spoel at xray.bmc.uu.se>
>     http://folding.bmc.uu.se
>     --
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>     What is the value for free energy of H-bonding.
>
>
>
>


-- 
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