[gmx-users] g_hbond

Chinmay Das chinmaydas71 at googlemail.com
Thu Aug 10 17:38:25 CEST 2006 

Dear David,
  ok. Now I understand HDA criterion. Can you give me a reference
where I can find the differences between HDA criteria and OHD criteria
and why one of them is preferable than the other?
  vmd certainly uses the later criteria. Changing the angle criteria
there  44 degrees in vmd picks up the bond that it was missing
earlier.
best regards
Chinmay

On 8/10/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 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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