[gmx-users] g_hbond

[Chinmay Das]

Dear Erik,
  Thanks a lot. with -nomerge, atleast I can see which atoms are involved.
[10 12 22] triplet, yes, distance is 0.297. But it should not go
through the angle criteria.
 R(10,12) = {0.088, 0.013, - 0.046}, |R(10,12)| = 0.10
 R(12,22) = {0.209, -0.018, 0.052}, |R(12,22)|=0.216
 R(10,12).R(12,22)=0.015766
 cos(angle)=R1.R2/(|R1| |R2|) = 0.7284
ie, the angle 43.2 degrees.
How did you get the angle 29.89 degrees?
best regards
Chinmay

On 8/10/06, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> It was a hard nut to crack, but I think I've done it after some sifting
> the source code:
>
> Since the -merge option is switched on by default, the hydrogen indexes
> are more or less irrelevant for some parts of the code. What happens
> here is that g_hbond finds the hbond [10 12 22] (distance: 0.2971
> nm, angle: 29.8925), but at a later point changes it into [10 11 22]
> during the merging, just like [22 24 16] turns into [22 23 16]. Note
> that the latter is apparent from the difference between what you find
> and the .ndx-file given below. Try running g_hbond -nomerge and you will
> see a slightly different ndx-file.
>
> One could debate whether this is really a bug or not, and the merging
> should in principle behave like this. I guess that an alternative is to
> completely omit the hydrogens when building the ndx-file using -merge to
> avoid confusion.
>
> A question arises: Why do VMD and yourself both find only 3 hbonds when
> there are four of them?
>
> /Erik
>
> On Wed, 2006-08-09 at 15:17 +0100, Chinmay Das wrote:
> > Hi,
> >   I am having trouble understanding the criteria for hydrogen bond and
> > how it is implemented in g_hbond. Defining hydrogen bond for O1--H..O2
> > by requiring distance(O1, O2) < 0.35 nm and angle(O1-H, H-O2) < 30
> > degrees, my own code consistently give lower number of hydrogen bonds
> > than g_hbond. But my results match if I count the hydrogen bonds
> > plotted with vmd using the same criteria. (To test this I created a
> > small system of water molecules at the center of a large box - so
> > periodic boundary condition is not the reason.)
> > Can some one help?
> >
> > Some details: I placed randomly oriented 8 SPC water on the vertices
> > of a cube with sides of size 0.3, starting at {x,y,z}={1.5,1.5,1.5}
> > and set the box length to be {4, 4, 4}. A very short NVT run at 30K
> > orients the water but doesn't move them much. vmd shows that the
> > configuration has 3 hydrogen bonds and my calculation also picks up
> > the same triplets and identifies as hydrogen bond. However, g_hbond
> > -hbn picks up 4. The hbonds_SOL entry in hbond.ndx have two of the
> > correct entries and two entries which seem wrong.
> >
> > hbond.ndx entry :
> > [ hbonds_SOL ]
> >       1      2     13
> >      10     11     22
> >      16     17     13
> >      22     23     16
> > What I find :
> > 1-2 -> 13
> > 16-17 -> 13
> > 22-24 -> 16
> >
> > And the configuration file :
> > Pure Water
> >    24
> >     1SOL     OW    1   1.494   1.496   1.495 -0.2407 -0.3859 -0.4517
> >     1SOL    HW1    2   1.593   1.511   1.498 -0.6476  3.2879  3.3372
> >     1SOL    HW2    3   1.470   1.416   1.551  0.4456  0.5879  1.2955
> >     2SOL     OW    4   1.506   1.503   1.801  0.3278  0.0764  0.1469
> >     2SOL    HW1    5   1.586   1.482   1.857  0.3064  1.6146  0.8017
> >     2SOL    HW2    6   1.435   1.434   1.817  0.1439  0.6902  2.4044
> >     3SOL     OW    7   1.499   1.810   1.507 -0.1617  0.6516  0.4652
> >     3SOL    HW1    8   1.446   1.767   1.579 -0.1540 -3.2274 -1.5277
> >     3SOL    HW2    9   1.439   1.833   1.430  0.5590 -2.0347 -1.0463
> >     4SOL     OW   10   1.499   1.802   1.796 -0.0922  0.1504 -0.2160
> >     4SOL    HW1   11   1.501   1.717   1.849 -2.8903 -1.0982 -1.9099
> >     4SOL    HW2   12   1.587   1.815   1.750  1.3885 -0.2196  2.3356
> >     5SOL     OW   13   1.798   1.491   1.501 -0.1855 -0.6306 -0.0502
> >     5SOL    HW1   14   1.856   1.410   1.508  2.6216  1.0980 -1.5287
> >     5SOL    HW2   15   1.813   1.535   1.412  0.8590  3.2110  1.8097
> >     6SOL     OW   16   1.804   1.499   1.803  0.1303 -0.0398  0.1705
> >     6SOL    HW1   17   1.771   1.492   1.709  2.6087  3.3512 -1.1639
> >     6SOL    HW2   18   1.865   1.423   1.824 -0.0578 -0.5609 -1.1170
> >     7SOL     OW   19   1.806   1.799   1.496  0.4549 -0.1262 -0.0397
> >     7SOL    HW1   20   1.762   1.879   1.537 -3.4166  1.6216 -6.2709
> >     7SOL    HW2   21   1.754   1.717   1.521 -3.2644  1.1647 -2.6085
> >     8SOL     OW   22   1.796   1.797   1.802 -0.2321 -0.1817  0.1797
> >     8SOL    HW1   23   1.830   1.847   1.722  3.7237 -1.1847  0.9954
> >     8SOL    HW2   24   1.808   1.699   1.788 -2.2397 -0.5892  0.9430
> >    4.00000   4.00000   4.00000
> >
> > Thanks in advance.
> > Chinmay
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> --
> Erik Marklund, PhD Student, Molecular Biopcysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone: +46 18 471 4537          fax: +46 18 511 755
> erikm at xray.bmc.uu.se
>
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