Re: [gmx-users] Segmentation fault in g_hbond

Erik Marklund wrote: leila karami skrev 2010-12-18 16.52: Dear Erik there are several hb->per->pHist in gmx_hbond.c. please say me exactly in which part of the gmx_hbond.c file if-statement should be placed? If I install gromacs 4.5.2 or 4.5.3, is there not this problem (segmentation fa

Re: [gmx-users] Segmentation fault in g_hbond

Erik Marklund skrev 2010-12-18 21.15: leila karami skrev 2010-12-18 16.52: Dear Erik there are several hb->per->pHist in gmx_hbond.c. please say me exactly in which part of the gmx_hbond.c file if-statement should be placed? If I install gromacs 4.5.2 or 4.5.3, is there not this problem (

Re: [gmx-users] Segmentation fault in g_hbond

leila karami skrev 2010-12-18 16.52: Dear Erik there are several hb->per->pHist in gmx_hbond.c. please say me exactly in which part of the gmx_hbond.c file if-statement should be placed? If I install gromacs 4.5.2 or 4.5.3, is there not this problem (segmentation fault)? -- Leila Karami

[gmx-users] Segmentation fault in g_hbond

Dear Erik there are several hb->per->pHist in gmx_hbond.c. please say me exactly in which part of the gmx_hbond.c file if-statement should be placed? If I install gromacs 4.5.2 or 4.5.3, is there not this problem (segmentation fault)? -- Leila Karami Ph.D. student of Physical Chemistry K.N.

Re: [gmx-users] Segmentation fault in g_hbond

Erik Marklund skrev 2010-12-18 16.36: Erik Marklund skrev 2010-12-18 16.23: leila karami skrev 2010-12-18 16.18: Dear Erik excuse me, I sent .xtc and .tpr file your e-mail. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistr

Re: [gmx-users] Segmentation fault in g_hbond

Erik Marklund skrev 2010-12-18 16.23: leila karami skrev 2010-12-18 16.18: Dear Erik excuse me, I sent .xtc and .tpr file your e-mail. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group I can reproduce the segfault.

Re: [gmx-users] Segmentation fault in g_hbond

leila karami skrev 2010-12-18 16.18: Dear Erik excuse me, I sent .xtc and .tpr file your e-mail. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group I can reproduce the segfault. It doesn't happen without -hbn. I'll ha

[gmx-users] Segmentation fault in g_hbond

Dear Erik excuse me, I sent .xtc and .tpr file your e-mail. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Plea

Re: [gmx-users] Segmentation fault in g_hbond

Erik Marklund skrev 2010-12-18 15.40: leila karami skrev 2010-12-18 15.38: Dear Erik thanks for your attention. in version 4.5.1, when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g -hbn, gromacs give me only hbnum.xvg with segmentation fault. when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g

Re: [gmx-users] Segmentation fault in g_hbond

leila karami skrev 2010-12-18 15.38: Dear Erik thanks for your attention. in version 4.5.1, when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g -hbn, gromacs give me only hbnum.xvg with segmentation fault. when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g, gromacs give me only hbnum.xvg witho

[gmx-users] Segmentation fault in g_hbond

Dear Erik thanks for your attention. in version 4.5.1, when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g -hbn, gromacs give me only hbnum.xvg with segmentation fault. when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g, gromacs give me only hbnum.xvg without segmentation fault. how to file a bug

Re: [gmx-users] Segmentation fault in g_hbond

Erik Marklund skrev 2010-12-18 15.02: leila karami skrev 2010-12-18 14.50: Dear Erik I used g_hbond in 4.5.1 but problem was not solved. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group Interesting. Could you file a

Re: [gmx-users] Segmentation fault in g_hbond

leila karami skrev 2010-12-18 14.50: Dear Erik I used g_hbond in 4.5.1 but problem was not solved. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group Interesting. Could you file a bugzilla and attach a tpr and xtc/trr

[gmx-users] Segmentation fault in g_hbond

Dear Erik I used g_hbond in 4.5.1 but problem was not solved. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Plea

Re: [gmx-users] Segmentation fault in g_hbond

Hi, Upgrade to 4.5.x and see if the problem persists. I've hacked g_hbond quite a bit since 4.0.5. Erik leila karami skrev 2010-12-18 14.02: Dear gromacs users I'm using gromacs 4.0.5. with following command: g_hbond -f .xtc -s .tpr -n .ndx -num -g -hbn. my system contains protein, dna an

[gmx-users] Segmentation fault in g_hbond

Dear gromacs users I'm using gromacs 4.0.5. with following command: g_hbond -f .xtc -s .tpr -n .ndx -num -g -hbn. my system contains protein, dna and water. when I use above command for protein and dna, there is no problem. segmentation fault is only for protein and water. -- Leila Karami Ph

[gmx-users] Segmentation fault in g_hbond

Dear gromacs users I used g_hbond tool for hydrogen bond analysis between protein and solvent (water molecules). I have encountered with : Select a group: 3 Selected 3: 'Protein' Select a group: 15 Selected 15: 'SOL' Checking for overlap in atoms between Protein and SOL Calculating hydrogen bon