[gmx-users] Segmentation fault from g_hbond
spoel at xray.bmc.uu.se
Fri Apr 9 16:39:01 CEST 2004
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.
> attached file:
> No option -da
> Reading file ezq_md.tpr, VERSION 3.2.1 (single
> Specify 2 groups to analyze:
> Opening library file
> 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 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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