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
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