Chinmay Das wrote:
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?
We implemented this in order to reproduce a number of publications. It
is difficult to say that one is to be preferred over the other. If
something an energy-based criterium could be preferred, however
classical mechanics is not good enough to quantitatively describe the
details of hydrogen bonding anyway. Some interesting refs are:
@Article{Starr2000a,
author = {F. W. Starr and J. K. Nielsen and H. Eugene Stanley},
title = {Hydrogen-bond dynamics for the extended simple point
charge model of water},
journal = {Phys. Rev. E},
year = 2000,
volume = 62,
pages = {579-587}
}
@Article{Modig2003a,
author = {K. Modig and B. G. Pfrommer and B. Halle},
title = {Temperature-dependent hydrogen bond geometry in liquid water},
journal = {Phys. Rev. Lett.},
year = 2003,
volume = 90,
pages = 075502
}
@Article{Spoel2006b,
author = {D. van der Spoel and P. J. van Maaren and P. Larsson and
N. Timneanu},
title = {Thermodynamics of hydrogen bonding in hydrophilic and
hydrophobic media},
journal = {J. Phys. Chem. B},
year = 2006,
volume = 110,
pages = {4393-4398}
}
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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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
>> [EMAIL PROTECTED]
>>
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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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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