[gmx-users] segmentation fault in gmx hbond

[Dr. D. H. Dagade]

Dear Gromacs users,
            I am doing hbond analysis of various organic anions after doing
successful free energy calculations with timestep of 2fs using GROMACS
2016.1 version. While using -ac option for autocorrelation, I got following
error.
Doing autocorrelation according to the theory of Luzar and Chandler.
Segmentation fault (core dumped)
Is it a bug or some mistake in calculations? I searched the gmx-mailing
archive  as well as on google for the solution but not got any clue. Can
anyone help me?
The details are given below:

  gmx hbond -f /run/media/dhd/Datadisk/dd/Free_energy/bimgly/ace/coul/
Lambda_20/Production_MD/md20.trr -s /run/media/dhd/Datadisk/dd/
Free_energy/bimgly/ace/coul/Lambda_20/Production_MD/md20.tpr -num -g -dist
-ang -hx -hbn -hbm -don -dan -life -nhbdist -ac

Reading file /run/media/dhd/Datadisk/dd/Free_energy/bimgly/ace/coul/
Lambda_20/Production_MD/md20.tpr, VERSION 2016 (single precision)
Specify 2 groups to analyze:
Group     0 (         System) has  3010 elements
Group     1 (          Other) has     7 elements
Group     2 (           ACEA) has     7 elements
Group     3 (          Water) has  3003 elements
Group     4 (            SOL) has  3003 elements
Group     5 (      non-Water) has     7 elements
Select a group: 2
Selected 2: 'ACEA'
Select a group: 3
Selected 3: 'Water'
Checking for overlap in atoms between ACEA and Water
Calculating hydrogen bonds between ACEA (7 atoms) and Water (3003 atoms)
Found 1001 donors and 1003 acceptors
Making hbmap structure...done.
trr version: GMX_trn_file (single precision)
Reading frame       0 time    0.000
Will do grid-seach on 8x8x5 grid, rcut=0.35
Frame loop parallelized with OpenMP using 32 threads.
Last frame       2000 time 2000.000
WARNING: Incomplete header: nr 2001 time 2000
Found 825 different hydrogen bonds in trajectory
Found 745 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
1001/1001
- Reduced number of hbonds from 825 to 825
- Reduced number of distances from 745 to 745
Average number of hbonds per timeframe 6.671 out of 502002 possible

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
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.
Segmentation fault (core dumped)

Is it a bug or some mistake in calculations? I searched the gmx-mailing
archive  as well as on google for the solution but not got any clue.

With Warm Regards,

Dr Dilip H Dagade,
Department of Chemistry,
Shivaji University,
Kolhapur 416004

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