[gmx-users] segmentation fault in gmx hbond

[David van der Spoel]

On 01/03/17 07:51, Dr. D. H. Dagade wrote:
> 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.

This has been fixed in 2016.2


> 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
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se