[gmx-users] g_hbond results inconsistent between v4.0.7 and v4.5.1

[Erik Marklund]

Hi,

No. But I hope to get it done this week. Thanks for the reminder.

Erik

Robin C. Underwood skrev 2010-12-05 19.19:
> Hi All:
>
> Has there been further resolution on the difference between g_hbond in v 4.0 and
> 4.5 (I'm running 4.5.3)? For counting water-water (tip4p) h-bonds in a box of
> 506 waters I get the following nhbdist output, which appears to neglect pbc
> since there are such a large number of unbound donor-H (and the other columns
> are consequently too low):
>
>
> @    title "Number of donor-H with N HBs"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "N"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "0 HBs"
> @ s1 legend "1 HB"
> @ s2 legend "2 HBs"
> @ s3 legend "3 HBs"
> @ s4 legend "Total"
>   0.00000e+00       706       174       132         0       438
>   1.00000e-01       708       163       140         1       446
>   2.00000e-01       707       168       137         0       442
>   3.00000e-01       712       161       136         3       442
>   4.00000e-01       713       165       134         0       433
>   5.00000e-01       709       169       133         1       438
>   6.00000e-01       705       169       137         1       446
>   7.00000e-01       699       169       142         2       459
>   8.00000e-01       710       167       133         2       439
>   9.00000e-01       700       189       122         1       436
>   1.00000e+00       707       169       136         0       441
>   1.10000e+00       705       163       144         0       451
>   1.20000e+00       707       171       133         1       440
>   1.30000e+00       709       158       145         0       448
>   1.40000e+00       718       155       138         1       434
>   1.50000e+00       711       164       137         0       438
>   1.60000e+00       713       160       139         0       438
>   1.70000e+00       702       181       129         0       439
>   1.80000e+00       707       162       142         1       449
>   1.90000e+00       706       167       139         0       445
>   2.00000e+00       709       168       135         0       438
>   2.10000e+00       708       167       136         1       442
>   2.20000e+00       708       171       133         0       437
>   2.30000e+00       709       162       140         1       445
>   2.40000e+00       698       171       142         1       458
>   2.50000e+00       701       177       133         1       446
>   2.60000e+00       706       177       129         0       435
>   2.70000e+00       708       178       126         0       430
>   2.80000e+00       698       187       127         0       441
>   2.90000e+00       700       190       120         2       436
>   3.00000e+00       703       176       131         2       444
>   3.10000e+00       702       181       127         2       441
>   3.20000e+00       694       184       134         0       452
>
>
> I've tried playing with different index assignments, and I get what appears to
> be a reasonable output for "0 HBs" by making the two groups appear different,
> excluding the dummy atom from one. Although, because the program then double
> counts, the other columns don't convey the intended information.
>
>
> Robin
>
>
>
>
>
>


-- 
-----------------------------------------------
Erik Marklund, PhD student
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    http://folding.bmc.uu.se/