[gmx-users] Error with editconf 4.0

[Justin A. Lemkul]

Hi all,

I was trying to dump out a .gro file from a .tpr under Gromacs 4.0, but editconf 
gave a Segmentation Fault.  The complete output is below:

editconf -f npt.tpr -o in.gro

<snip>

Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
WARNING: masses will be determined based on residue and atom names,
          this can deviate from the real mass of the atom type
Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
Entries in atommass.dat: 178
WARNING: vdwradii will be determined based on residue and atom names,
          this can deviate from the real mass of the atom type
Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 31
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading file npt.tpr, VERSION 4.0 (single precision)
Reading file npt.tpr, VERSION 4.0 (single precision)
editconf(12411) malloc: *** error for object 0x1006e00: incorrect checksum for 
freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug
editconf(12411) malloc: *** error for object 0x100ce00: incorrect checksum for 
freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug
editconf(12411) malloc: *** error for object 0x9070b0: double free
*** set a breakpoint in malloc_error_break to debug
editconf(12411) malloc: *** error for object 0x1002400: double free
*** set a breakpoint in malloc_error_break to debug
editconf(12411) malloc: *** error for object 0x100ce00: double free
*** set a breakpoint in malloc_error_break to debug
editconf(12411) malloc: *** error for object 0x907330: double free
*** set a breakpoint in malloc_error_break to debug
editconf(12411) malloc: *** error for object 0x907ad0: double free
*** set a breakpoint in malloc_error_break to debug
editconf(12411) malloc: *** error for object 0x907ba0: double free
*** set a breakpoint in malloc_error_break to debug
editconf(12411) malloc: *** error for object 0x907c40: double free
*** set a breakpoint in malloc_error_break to debug
editconf(12411) malloc: *** error for object 0x130000: pointer being freed was 
not allocated
*** set a breakpoint in malloc_error_break to debug
Read 138271 atoms
Volume: 1701.6 nm^3, corresponds to roughly 765700 electrons
Velocities found
editconf(12411) malloc: *** error for object 0x100ce00: incorrect checksum for 
freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug
editconf(12411) malloc: *** error for object 0x907c50: incorrect checksum for 
freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug
Segmentation fault

No output is generated, obviously.  Interestingly, if I issue the same command 
with editconf 4.0 on a .tpr file generated under Gromacs 3.3.3, I get the following:

<snip>

Reading file npt.tpr, VERSION 3.3.3 (single precision)
Reading file npt.tpr, VERSION 3.3.3 (single precision)
editconf(12421) malloc: *** error for object 0x2316000: pointer being freed was 
not allocated
*** set a breakpoint in malloc_error_break to debug
editconf(12421) malloc: *** error for object 0xf8c000: pointer being freed was 
not allocated
*** set a breakpoint in malloc_error_break to debug
editconf(12421) malloc: *** error for object 0x27d6000: pointer being freed was 
not allocated
*** set a breakpoint in malloc_error_break to debug
editconf(12421) malloc: *** error for object 0x2cee000: pointer being freed was 
not allocated
*** set a breakpoint in malloc_error_break to debug
editconf(12421) malloc: *** error for object 0x296e000: pointer being freed was 
not allocated
*** set a breakpoint in malloc_error_break to debug
editconf(12421) malloc: *** error for object 0x29f6000: pointer being freed was 
not allocated
*** set a breakpoint in malloc_error_break to debug
editconf(12421) malloc: *** error for object 0x2bde000: pointer being freed was 
not allocated
*** set a breakpoint in malloc_error_break to debug
editconf(12421) malloc: *** error for object 0x1006a00: double free
*** set a breakpoint in malloc_error_break to debug
editconf(12421) malloc: *** error for object 0xfb4000: pointer being freed was 
not allocated
*** set a breakpoint in malloc_error_break to debug
editconf(12421) malloc: *** error for object 0x2c34000: pointer being freed was 
not allocated
*** set a breakpoint in malloc_error_break to debug
editconf(12421) malloc: *** error for object 0x180000: pointer being freed was 
not allocated
*** set a breakpoint in malloc_error_break to debug
editconf(12421) malloc: *** error for object 0xfdd000: pointer being freed was 
not allocated
*** set a breakpoint in malloc_error_break to debug
editconf(12421) malloc: *** error for object 0x2c66000: pointer being freed was 
not allocated
*** set a breakpoint in malloc_error_break to debug
editconf(12421) malloc: *** error for object 0x2ca1000: pointer being freed was 
not allocated
*** set a breakpoint in malloc_error_break to debug
editconf(12421) malloc: *** error for object 0x1002400: double free
*** set a breakpoint in malloc_error_break to debug
editconf(12421) malloc: *** error for object 0x9071c0: double free
*** set a breakpoint in malloc_error_break to debug
editconf(12421) malloc: *** error for object 0x2d24000: pointer being freed was 
not allocated
*** set a breakpoint in malloc_error_break to debug
Read 138271 atoms
Volume: 2001.49 nm^3, corresponds to roughly 900600 electrons
Velocities found

gcq#163: "If You Don't Like Cool Quotes Check Your GMXRC File" (Your Sysadmin)

The result is that in.gro is generated from the 3.3.3 .tpr file.  Any ideas 
what's going on?

Thanks,
Justin

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================