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Hi,<br>
<br>
That is another small bug in the 4.0 release.<br>
I had already fixed this for 4.0.1.<br>
<br>
Berk<br><br><br>> Date: Wed, 5 Nov 2008 17:19:34 -0500<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Error with editconf 4.0<br>> <br>> <br>> Hi all,<br>> <br>> I was trying to dump out a .gro file from a .tpr under Gromacs 4.0, but editconf <br>> gave a Segmentation Fault. The complete output is below:<br>> <br>> editconf -f npt.tpr -o in.gro<br>> <br>> <snip><br>> <br>> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>> WARNING: masses will be determined based on residue and atom names,<br>> this can deviate from the real mass of the atom type<br>> Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat<br>> Entries in atommass.dat: 178<br>> WARNING: vdwradii will be determined based on residue and atom names,<br>> this can deviate from the real mass of the atom type<br>> Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat<br>> Entries in vdwradii.dat: 31<br>> Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat<br>> Entries in dgsolv.dat: 7<br>> Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat<br>> Entries in electroneg.dat: 71<br>> Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat<br>> Entries in elements.dat: 218<br>> Reading file npt.tpr, VERSION 4.0 (single precision)<br>> Reading file npt.tpr, VERSION 4.0 (single precision)<br>> editconf(12411) malloc: *** error for object 0x1006e00: incorrect checksum for <br>> freed object - object was probably modified after being freed.<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12411) malloc: *** error for object 0x100ce00: incorrect checksum for <br>> freed object - object was probably modified after being freed.<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12411) malloc: *** error for object 0x9070b0: double free<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12411) malloc: *** error for object 0x1002400: double free<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12411) malloc: *** error for object 0x100ce00: double free<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12411) malloc: *** error for object 0x907330: double free<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12411) malloc: *** error for object 0x907ad0: double free<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12411) malloc: *** error for object 0x907ba0: double free<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12411) malloc: *** error for object 0x907c40: double free<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12411) malloc: *** error for object 0x130000: pointer being freed was <br>> not allocated<br>> *** set a breakpoint in malloc_error_break to debug<br>> Read 138271 atoms<br>> Volume: 1701.6 nm^3, corresponds to roughly 765700 electrons<br>> Velocities found<br>> editconf(12411) malloc: *** error for object 0x100ce00: incorrect checksum for <br>> freed object - object was probably modified after being freed.<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12411) malloc: *** error for object 0x907c50: incorrect checksum for <br>> freed object - object was probably modified after being freed.<br>> *** set a breakpoint in malloc_error_break to debug<br>> Segmentation fault<br>> <br>> No output is generated, obviously. Interestingly, if I issue the same command <br>> with editconf 4.0 on a .tpr file generated under Gromacs 3.3.3, I get the following:<br>> <br>> <snip><br>> <br>> Reading file npt.tpr, VERSION 3.3.3 (single precision)<br>> Reading file npt.tpr, VERSION 3.3.3 (single precision)<br>> editconf(12421) malloc: *** error for object 0x2316000: pointer being freed was <br>> not allocated<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12421) malloc: *** error for object 0xf8c000: pointer being freed was <br>> not allocated<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12421) malloc: *** error for object 0x27d6000: pointer being freed was <br>> not allocated<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12421) malloc: *** error for object 0x2cee000: pointer being freed was <br>> not allocated<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12421) malloc: *** error for object 0x296e000: pointer being freed was <br>> not allocated<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12421) malloc: *** error for object 0x29f6000: pointer being freed was <br>> not allocated<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12421) malloc: *** error for object 0x2bde000: pointer being freed was <br>> not allocated<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12421) malloc: *** error for object 0x1006a00: double free<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12421) malloc: *** error for object 0xfb4000: pointer being freed was <br>> not allocated<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12421) malloc: *** error for object 0x2c34000: pointer being freed was <br>> not allocated<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12421) malloc: *** error for object 0x180000: pointer being freed was <br>> not allocated<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12421) malloc: *** error for object 0xfdd000: pointer being freed was <br>> not allocated<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12421) malloc: *** error for object 0x2c66000: pointer being freed was <br>> not allocated<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12421) malloc: *** error for object 0x2ca1000: pointer being freed was <br>> not allocated<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12421) malloc: *** error for object 0x1002400: double free<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12421) malloc: *** error for object 0x9071c0: double free<br>> *** set a breakpoint in malloc_error_break to debug<br>> editconf(12421) malloc: *** error for object 0x2d24000: pointer being freed was <br>> not allocated<br>> *** set a breakpoint in malloc_error_break to debug<br>> Read 138271 atoms<br>> Volume: 2001.49 nm^3, corresponds to roughly 900600 electrons<br>> Velocities found<br>> <br>> gcq#163: "If You Don't Like Cool Quotes Check Your GMXRC File" (Your Sysadmin)<br>> <br>> The result is that in.gro is generated from the 3.3.3 .tpr file. Any ideas <br>> what's going on?<br>> <br>> Thanks,<br>> Justin<br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Graduate Research Assistant<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? 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