[gmx-users] Segmentation fault from g_hbond

[xiaobing tian]

Dear GMX users,

After 1ns MD for my system (protein+drug(RPR)+ Ca2+ +
Cl-), g_hbond -f file.xtc -s file.tpr -num hydrogen.xvg  
gave a Segmentation faut (see attached file below) and
then stopped. How to fix the problem?( I use gmx3.2.1,
Linux Red Hat8.0) 

Thank you very much for your reply.

Xiaobing

attached file:
No option -da
Reading file ezq_md.tpr, VERSION 3.2.1 (single
precision)
Specify 2 groups to analyze:
Opening library file
/usr/local/share/gromacs/top/aminoacids.dat
Group     0 (      System) has 47436 elements
Group     1 (     Protein) has  2869 elements
Group     2 (   Protein-H) has  2229 elements
Group     3 (     C-alpha) has   285 elements
Group     4 (    Backbone) has   855 elements
Group     5 (   MainChain) has  1142 elements
Group     6 (MainChain+Cb) has  1400 elements
Group     7 ( MainChain+H) has  1422 elements
Group     8 (   SideChain) has  1447 elements
Group     9 ( SideChain-H) has  1087 elements
Group    10 ( Prot-Masses) has  2869 elements
Group    11 ( Non-Protein) has 44567 elements
Group    12 (          CA) has     1 elements
Group    13 (         RPR) has    42 elements
Group    14 (         SOL) has 44523 elements
Group    15 (          Cl) has     1 elements
Group    16 (       Other) has 44567 elements
Select a group: 13
Selected 13: 'RPR'
Select a group: 1
Selected 1: 'Protein'
Checking for overlap...
Calculating hydrogen bonds between two groups of 42
and 2869 atoms
Found 4 donors and 7 acceptors in group 'RPR'
Found 419 donors and 817 acceptors in group 'Protein'
Going to allocate 8169 kb of memory,  and that's only
the beginning
trn version: GMX_trn_file (single precision)
Reading frame       0 time    0.000
Will do grid-seach on 18x18x18 grid, rcut=0.35
Last frame        250 time 1000.000
Found 13 different hydrogen bonds in trajectory
Merging hbonds with Acceptor and Donor swapped
Segmentation fault (core dumped)
[root at tesla ezq]#



Xiaobing Tian  Ph.D.
Department of Microbiology and Immunology
Thomas Jefferson University
1025 Walnut St., Suite 420
Philadelphia,  PA19107
Phone: 215-955-1364 (Lab)

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