[gmx-users] Segmentation fault from g_hbond

[David]

On Fri, 2004-04-09 at 16:19, xiaobing tian wrote:
> 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) 
you could try g_hbond -nomerge
the number of hbonds is still correct then.

A fix will be included in the next version.

> 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 a nd Immunology
> Thomas Jefferson University
> 1025 Walnut St., Suite 420
> Philadelphia, PA19107
> Phone: 215-955-1364 (Lab)
> 
> 
> ______________________________________________________________________
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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