[gmx-users] gmx covar: Segmentation fault
Oliwia Maria Szklarczyk
oliwias at ethz.ch
Wed Apr 20 16:51:35 CEST 2016
Dear All,
Anyone has experience with the covariance analysis program from gromacs? I can’t get rid of the segmentation fault. I run the following:
gmx covar -f md.xtc -s md.tpr -v eigenvec.trr -n sys.ndx
And this is the output:
Choose a group for the least squares fit
Group 0 ( Ligand) has 121 elements
Group 1 ( Ligand-C-alpha) has 12 elements
Group 2 ( EB1) has 1370 elements
Group 3 ( System) has 88911 elements
Group 4 ( Protein) has 1491 elements
Group 5 ( Protein-H) has 1194 elements
Group 6 ( C-alpha) has 149 elements
Group 7 ( Backbone) has 446 elements
Group 8 ( MainChain) has 596 elements
Group 9 ( MainChain+Cb) has 734 elements
Group 10 ( MainChain+H) has 739 elements
Group 11 ( SideChain) has 752 elements
Group 12 ( SideChain-H) has 598 elements
Group 13 ( Prot-Masses) has 1491 elements
Group 14 ( non-Protein) has 87420 elements
Group 15 ( Water) has 87402 elements
Group 16 ( SOL) has 87402 elements
Group 17 ( non-Water) has 1509 elements
Group 18 ( Ion) has 18 elements
Group 19 ( NA) has 18 elements
Group 20 ( Water_and_ions) has 87420 elements
Select a group: 1
Selected 1: 'Ligand-C-alpha'
Choose a group for the covariance analysis
Group 0 ( Ligand) has 121 elements
Group 1 ( Ligand-C-alpha) has 12 elements
Group 2 ( EB1) has 1370 elements
Group 3 ( System) has 88911 elements
Group 4 ( Protein) has 1491 elements
Group 5 ( Protein-H) has 1194 elements
Group 6 ( C-alpha) has 149 elements
Group 7 ( Backbone) has 446 elements
Group 8 ( MainChain) has 596 elements
Group 9 ( MainChain+Cb) has 734 elements
Group 10 ( MainChain+H) has 739 elements
Group 11 ( SideChain) has 752 elements
Group 12 ( SideChain-H) has 598 elements
Group 13 ( Prot-Masses) has 1491 elements
Group 14 ( non-Protein) has 87420 elements
Group 15 ( Water) has 87402 elements
Group 16 ( SOL) has 87402 elements
Group 17 ( non-Water) has 1509 elements
Group 18 ( Ion) has 18 elements
Group 19 ( NA) has 18 elements
Group 20 ( Water_and_ions) has 87420 elements
Select a group: 0
Selected 0: 'Ligand'
Calculating the average structure ...
Last frame 300 time 30000.000
Back Off! I just backed up average.pdb to ./#average.pdb.8#
Constructing covariance matrix (363x363) ...
Last frame 300 time 30000.000
Read 301 frames
Trace of the covariance matrix: 7.96121 (nm^2)
Diagonalizing ...
Sum of the eigenvalues: 7.96121 (nm^2)
[euler04:19031] *** Process received signal ***
[euler04:19031] Signal: Segmentation fault (11)
[euler04:19031] Signal code: Address not mapped (1)
[euler04:19031] Failing at address: (nil)
[euler04:19031] [ 0] /lib64/libpthread.so.0(+0xf7e0) [0x7f5112b257e0]
[euler04:19031] [ 1] /lib64/libc.so.6(fwrite+0x34) [0x7f51120bc974]
[euler04:19031] [ 2] /cluster/apps/gromacs/5.0.2/x86_64/gcc_4.8.2/openmpi_1.6.5/bin/../lib64/libgromacs_mpi.so.0(gmx_covar+0x3cc9) [0x7f5116c79a69]
[euler04:19031] [ 3] /cluster/apps/gromacs/5.0.2/x86_64/gcc_4.8.2/openmpi_1.6.5/bin/../lib64/libgromacs_mpi.so.0(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x8a) [0x7f5116a09cfa]
[euler04:19031] [ 4] gmx_mpi(main+0x85) [0x40cc25]
[euler04:19031] [ 5] /lib64/libc.so.6(__libc_start_main+0xfd) [0x7f5112073d5d]
[euler04:19031] [ 6] gmx_mpi() [0x40c419]
[euler04:19031] *** End of error message ***
Segmentation fault
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