[gmx-users] Re: hydrogen bonds in water tutorial

[Sung Hyun Park]

Thank you so much for the answer, Prof. van der Spoel.

Now I'd like to ask two more questions to you and all gmx-users.

First, I notice that the number of hydrogen bonds for a given time
frame fluctuates slightly, depending on the time range you choose in
g_hbond command.

For example, in the same "water" tutorial, if I do the following command:
> g_hbond
the hbnum.xvg looks like this:
        19         363         746
      19.1         366         714
      19.2         360         696

      19.3         371         720
      19.4         355         701
      19.5         357         686
      19.6         357         711
      19.7         351         702
      19.8         351         712

      19.9         360         673
        20         363         716
However, if I do the following command:
> g_hbond -b 18.99 -e 20
the hbnum.xvg now looks like this:
        19         367         754

      19.1         365         715
      19.2         358         702
      19.3         371         723
      19.4         354         714
      19.5         369         699
      19.6         357         711

      19.7         355         700
      19.8         351         712
      19.9         367         699
        20         367         727
And if I do:
>g_hbond -b 19.99 -e 20
the hbnum.xvg now looks like this:

        20         358         715
You see the number of hydrogen bonds for a given time are different
for each command.
I wonder why this happens and if there is any significance in it.

My second question is a bit more complicated.

I'm trying to calculate the average number of hbonds per time frame as
a function of z coordinates for two time frames, say t=19.9 and t=20,
in the "water" tutorial.
So I'm thinking of first creating the index file of hbonds by doing:

> g_hbond -hbn -b 19.9 -e 20
, then extracting z coordinates of all the atoms involved in hydrogen
bonds at each time frame using g_traj command.
Now, at the end of the g_hbond execution, I see the following gromacs comments:

------------------------------------------------------------
Reading frame       0 time   19.900
Will do grid-seach on 4x4x4 grid, rcut=0.35
Last frame          1 time   20.000
Found 422 different hydrogen bonds in trajectory

------------------------------------------------------------
And the hbond.ndx files indeed lists the 422 "different" hydrogen bonds,
However the last two lines of the hbnum.xvg shows:
      19.9         358         683

        20         365         726
which means that there are 358+365 = 723 hbonds over the two time
frames. I guess that 422 hbonds in index file count those duplicate
hbonds over two time frames only once.
Does that mean that I cannot use the hbond.ndx file to properly count
total number of hbonds (723) over two time frames?

If so, do I need to obtain hbond.ndx for each single time frame
separately to calculate the average number of hbonds per time frame
along z axis correctly?

I hope my questions are clear.
Thank you in advance for your kind reply.

Regards,
Sung


Sung Hyun Park wrote:
>* Dear Gmx-users,
*>*
*>* This may be a dumb question, but I am wondering about the number of
*>* hydrogen bonds in the "water" tutorial. The system is 216 SPC/E water
*>* molecules in a box, and the number of hydrogen bonds per time frame
*>* fluctuates around ~350, which gives th number of hydrogen bonds per
*>* water mlecule to be only ~1.6. Isn't this too low, compared with the
*>* typical number ~3.5 for bulk water mlecule?
*I think it is SPC, and you can multiply the number by 2 since all HB are
shared between two mols.
>*
*>* Thanks,
*>* Sung
*>*
*>*
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.

Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se
<http://www.gromacs.org/mailman/listinfo/gmx-users>	spoel at
gromacs.org <http://www.gromacs.org/mailman/listinfo/gmx-users>
http://folding.bmc.uu.se
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