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 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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] _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php