Archive from user: Stéphane Abel I report an issue with gmx mindist of gromacs (v 4.6.7, 5.1.4 and 2018+). The program crashes with the following command echo 0 1 >Protein\_AlkylChain.txt - gmx\_mpi mindist -f myXTC.xtc -s MYPDB.pdb -n Hydratation\_Protein\_OGNG.ndx -b 215000 -e 215000 -dt 4 -d 0.4 -respertime -printresname -group -od 3FHH\_102OGNG\_complex\_CHARMM36\_TIP3P\_Protein\_AlkylChain\_Contact\_min\_res.xvg -on 3FHH\_102OGNG\_complex\_CHARMM36\_TIP3P\_Protein\_AlkylChain\_Contact\_Number.xvg < Protein\_AlkylChain.txt With GMX4.6.7 —>OK With GMX5.1.4 (segmentation fault) ——————————— Group 0 (Protein\_HeavyAtoms) has 4976 elements Group 1 (OGNG\_AlkylChain) has 1530 elements Group 2 ( OGNG\_Headgroup) has 2244 elements Group 3 (OGNG\_All\_HeavyAtoms) has 3774 elements Group 4 ( Water\_oxygen) has 60000 elements Select a group: Select a group: ^MReading frame 0 time 0.000 ^MReading frame 0 time 200000.000 Back Off! I just backed up 3FHH\_102OGNG\_complex\_CHARMM36\_TIP3P\_Protein\_AlkylChain\_Contact\_min\_res.xvg to ./\#3FHH\_102OGNG\_complex\_CHARMM36\_TIP3P\_Protein\_AlkylChain\_Contact\_min\_res.xvg.2\# Back Off! I just backed up 3FHH\_102OGNG\_complex\_CHARMM36\_TIP3P\_Protein\_AlkylChain\_Contact\_Number.xvg to ./\#3FHH\_102OGNG\_complex\_CHARMM36\_TIP3P\_Protein\_AlkylChain\_Contact\_Number.xvg.2\# \[irene1022:52095:0\] Caught signal 11 (Segmentation fault) backtrace 2 0x0000000000068d1c mxm\_handle\_error() /var/tmp/OFED\_topdir/BUILD/mxm-3.6.3102/src/mxm/util/debug/debug.c:641 3 0x000000000006926c mxm\_error\_signal\_handler() /var/tmp/OFED\_topdir/BUILD/mxm-3.6.3102/src/mxm/util/debug/debug.c:616 4 0x0000000000035270 killpg() ??:0 5 0x00000000000471ad \_IO\_vfprintf\_internal() :0 6 0x0000000000051827 \_\_GI\_fprintf() :0 7 0x00000000003b3cd8 xvgr\_header() ??:0 8 0x00000000003b3c70 xvgropen\_type() ??:0 9 0x0000000000545400 dist\_plot.a() gmx\_mindist.c:0 10 0x0000000000543990 gmx\_mindist() ??:0 11 0x00000000001e1ff3 \_ZN3gmx24Comman With GMX2018 and 2018.2 (fatal error) ——————————— Group 0 (Protein\_HeavyAtoms) has 4976 elements Group 1 (OGNG\_AlkylChain) has 1530 elements Group 2 ( OGNG\_Headgroup) has 2244 elements Group 3 (OGNG\_All\_HeavyAtoms) has 3774 elements Group 4 ( Water\_oxygen) has 60000 elements Select a group: Select a group: ^MReading frame 0 time 0.000 ^MReading frame 0 time 200000.000 Back Off! I just backed up 3FHH\_102OGNG\_complex\_CHARMM36\_TIP3P\_Protein\_AlkylChain\_Contact\_min\_res.xvg to ./\#3FHH\_102OGNG\_complex\_CHARMM36\_TIP3P\_Protein\_AlkylChain\_Contact\_min\_res.xvg.1\# Back Off! I just backed up 3FHH\_102OGNG\_complex\_CHARMM36\_TIP3P\_Protein\_AlkylChain\_Contact\_Number.xvg to ./\#3FHH\_102OGNG\_complex\_CHARMM36\_TIP3P\_Protein\_AlkylChain\_Contact\_Number.xvg.1\# ------------------------------------------------------------------------ Program: gmx mindist, version 2018 Source file: src/gromacs/fileio/gmxfio.cpp (line 345) Fatal error: Cannot open file with NULL filename string For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ———————————————————————————- + echo 0 2 + echo 0 3 + echo 0 4 + exit 0 Please note that if I remove the “-group” and “-printresname” arguments all the tested version (except for 4.6.7) crashes. I have included three files for the tests MYXTC.xtc (1 snapshot 215ns) MYNDX.ndx MYPDB.pdb Thank you *(from redmine: issue id 2653, created on 2018-09-26 by gmxdefault, closed on 2018-10-04)* * Changesets: * Revision 034183c82d46d45981ef9543a77c80193b3f72ac by Paul Bauer on 2018-09-27T14:37:13Z: ``` Add mindist output file check gmx mindist would not check if the output file for an analysis options was actually present, leading to cryptic error messages. Added the corresponding check. Fixes #2653 Change-Id: I26ccc7df37e5cc6a0276ecce50036aba452e0a45 ``` * Uploads: * [MYPDB.pdb](/uploads/e4f49a3de7c438feb703e1332521a45e/MYPDB.pdb) PDB of the system * [MYXTC.xtc](/uploads/acae398468463b07e70019b5ac1da751/MYXTC.xtc) Trajectory file (1 frame, 215 ns) * [MYNDX.ndx](/uploads/a59ff1c8880e2440d27eec3193f05357/MYNDX.ndx) index file with different subsystem * [MYNDX.ndx](/uploads/56926dd5f61aed7a317fd190a56c4408/MYNDX.ndx) index file with different subsystems * [MYXTC.xtc](/uploads/180621b53c45d86cd2ff849b2fc0c0ce/MYXTC.xtc) Trajectory file (1 frame, 215 ns) * [MYPDB.pdb](/uploads/c7df40ac6f18d4a9a377d2e6a50f1853/MYPDB.pdb) PDB of the system