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Bug #78

g_rdf on OS X 10.3.9 (segmentation fault)

Added by Sukit Leekumjorn over 13 years ago. Updated over 13 years ago.

Status:
Closed
Priority:
High
Assignee:
Erik Lindahl
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

Both Gromacs 3.3 and 3.3.1 have the same problem with g_rdf. Other analysis
tools seem to work fine. Below is the symtom from both version of Gromacs. No
output is written.

5/8/2006

:-)  G  R  O  M  A  C  S  (-:
Good ROcking Metal Altar for Chronical Sinners
:-)  VERSION 3.3  (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-)  g_rdf_3.3_s  (-:

Option Filename Type Description
------------------------------------------------------------
-f dppc256_1.xtc Input Generic trajectory: xtc trr trj gro g96 pdb
-s dppc256_1.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
xml
-n dppc256_system.ndx Input, Opt! Index file
-o test.xvg Output, Opt! xvgr/xmgr file
-sq sq.xvg Output, Opt. xvgr/xmgr file
-cn rdf_cn.xvg Output, Opt. xvgr/xmgr file
-hq hq.xvg Output, Opt. xvgr/xmgr file

Option   Type  Value  Description
------------------------------------------------------
h bool no Print help info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 100 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-bin real 0.002 Binwidth (nm)
-[no]com bool no RDF with respect to the center of mass of first
group
-[no]pbc bool yes Use periodic boundary conditions for computing
distances
-[no]xy bool no Use only the x and y components of the distance
-cut real 0 Shortest distance (nm) to be considered
-ng int 1 Number of secondary groups to compute RDFs around
a central group
-fade real 0 From this distance onwards the RDF is tranformed
by g'(r) = 1 + [g(r)-1] exp(
(r/fade-1)^2 to make
it go to 1 smoothly. If fade is 0.0 nothing is
done.
-nlevel int 20 Number of different colors in the diffraction
image
-startq real 0 Starting q (1/nm)
-endq real 60 Ending q (1/nm)
-energy real 12 Energy of the incoming X-ray (keV)

Reading file dppc256_1.tpr, VERSION 3.3 (double precision)
Reading file dppc256_1.tpr, VERSION 3.3 (double precision)

Select a reference group and 1 group
Group 0 ( System) has 35840 elements
Group 1 ( DPPC) has 12800 elements
Group 2 ( WAT) has 23040 elements
Group 3 ( P8) has 256 elements
Select a group: 3
Selected 3: 'P8'
Select a group: 3
Selected 3: 'P8'
Reading frame 40 time 80.000

Segmentation fault

:-)  G  R  O  M  A  C  S  (-:
GRoups of Organic Molecules in ACtion for Science
:-)  VERSION 3.3.1  (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2006, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-)  g_rdf_3.3.1_s  (-:

Option Filename Type Description
------------------------------------------------------------
-f dppc256_1.xtc Input Generic trajectory: xtc trr trj gro g96 pdb
-s dppc256_1.tpr Input, Opt! Structure+mass(db): tpr tpb tpa gro g96 pdb
xml
-n dppc256_system.ndx Input, Opt! Index file
-o test.xvg Output, Opt! xvgr/xmgr file
-sq sq.xvg Output, Opt. xvgr/xmgr file
-cn rdf_cn.xvg Output, Opt. xvgr/xmgr file
-hq hq.xvg Output, Opt. xvgr/xmgr file

Option   Type  Value  Description
------------------------------------------------------
h bool no Print help info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 100 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-bin real 0.002 Binwidth (nm)
-[no]com bool no RDF with respect to the center of mass of first
group
-[no]pbc bool yes Use periodic boundary conditions for computing
distances
-[no]xy bool no Use only the x and y components of the distance
-cut real 0 Shortest distance (nm) to be considered
-ng int 1 Number of secondary groups to compute RDFs around
a central group
-fade real 0 From this distance onwards the RDF is tranformed
by g'(r) = 1 + [g(r)-1] exp(
(r/fade-1)^2 to make
it go to 1 smoothly. If fade is 0.0 nothing is
done.
-nlevel int 20 Number of different colors in the diffraction
image
-startq real 0 Starting q (1/nm)
-endq real 60 Ending q (1/nm)
-energy real 12 Energy of the incoming X-ray (keV)

Reading file dppc256_1.tpr, VERSION 3.3 (double precision)
Reading file dppc256_1.tpr, VERSION 3.3 (double precision)

Select a reference group and 1 group
Group 0 ( System) has 35840 elements
Group 1 ( DPPC) has 12800 elements
Group 2 ( WAT) has 23040 elements
Group 3 ( P8) has 256 elements
Select a group: 3
Selected 3: 'P8'
Select a group: 3
Selected 3: 'P8'
Reading frame 40 time 80.000

Segmentation fault

History

#1 Updated by David van der Spoel over 13 years ago

Same as bug 77.

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