[gmx-users] segmentation fault in gmx hbond

[Tasneem Kausar]

Check your hbnum.xvg file. Probably you calculation has been completed
successfully.


On Wed, Mar 1, 2017 at 12:21 PM, Dr. D. H. Dagade <dhd_chem at unishivaji.ac.in
> 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.
> 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
>
> --
> This email and any files transmitted with it are confidential and intended
> solely for the use of the individual or entity to whom they are addressed.
> If you have received this email in error please notify the system manager.
> Please note that any views or opinions presented in this email are solely
> those of the author and do not necessarily represent those of the Shivaji
> University. Finally, the recipient should check this email and any
> attachments for the presence of viruses. Shivaji University accepts no
> liability for any damage caused by any virus transmitted by this email.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>