Bug #1553

Updated by Mark Abraham about 6 years ago


i found that using g_hbond as in:

g_hbond -f traj.xtc -s topol.tpr -n index.ndx -ac -smooth 1

gives me a seg-fault (see for example the stdout below)
i did not include/upload any input files because the files i used tend
to be huge. However this should be reproducible anyway as it seems to be a general issue:
I get the same error for a number of widely different systems, e.g., a polymer blend or
a protein in aqueous solution ...

this happens both with single and double precision (both for the
g_hbond and the trajectory versions) and also for both
g_hbond from gmx-4.6.5 and gmx-5.0-beta2 (the latter with single prec
i seem to recall ... gmx -h wouldn't tell me ...)

if i do not use the smooth option but leave everything else
the same then the segfault goes away ...


below a typical stdout of g_hbond -f traj.xtc -s topol.tpr -n index.ndx -ac -smooth 1
Select a group: 1
Selected 1: 'Protein'
Select a group: 20
Selected 20: 'Water'
Checking for overlap in atoms between Protein and Water
Calculating hydrogen bonds between Protein (4899 atoms) and Water (23835 atoms)
Found 8389 donors and 8833 acceptors
Making hbmap structure...done.
Reading frame 0 time 0.000
Will do grid-seach on 15x15x15 grid, rcut=0.35
Frame loop parallelized with OpenMP using 8 threads.
Last frame 5000 time 2000.000
Found 88942 different hydrogen bonds in trajectory
Found 181742 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
- Reduced number of hbonds from 88942 to 83886
- Reduced number of distances from 181742 to 181742

Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.1#
Average number of hbonds per timeframe 578.545 out of 3.705e+07 possible

D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu
Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media
J. Phys. Chem. B 110 (2006) pp. 4393-4398
-------- -------- --- Thank You --- -------- --------

Doing autocorrelation according to the theory of Luzar and Chandler.
ACF 83886/83886
Normalization for c(t) = 0.00172792 for gh(t) = 3.45631e-07

WARNING: Correlation function is probably not long enough
because the standard deviation in the tail of C(t) > 0.001
Tail value (average C(t) over second half of acf): 0.0786273 +/- 0.00446663
Segmentation fault (core dumped)