# [gmx-users] g_hbond

David van der Spoel spoel at xray.bmc.uu.se
Thu Aug 10 17:20:10 CEST 2006

Chinmay Das wrote:
> 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?

you're computing a different angle. g_hbond uses HDA, or in your
numbering 12-10-22, that is you have to compute vectors 10-12 and 10-22

> 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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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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