[gmx-users] QM/MM-ORCA Point Charge Correction Error

Zoe Chan 15901671r at connect.polyu.hk
Mon Nov 27 10:14:19 CET 2017

Dear Gromacs Users,

I've been running a QM/MM calculation on a protein with fluorescence probe, using gromacs 4.6.7 (double precision with MPI) and ORCA 4.0.1.  The following lines were included in the .mdp file,

QMMM                     = yes
QMMM-grps            = QMatoms
QMmethod              = B3LYP
QMbasis                  = 6-31G*
QMMMscheme       = ONIOM
QMcharge               = -2
QMmult                    = 2

The run was aborted with the error messages,

Filename: temp.pc

*** Process received signal ***
Signal: Segmentation fault (11)
Signal code: Address not mapped (1)
Failing at address: (nil)
[ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x2ba5c5ada390]
[ 1] /lib/x86_64-linux-gnu/libc.so.6(fgets+0x1e)[0x2ba5c5d53aee]
[ 2] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(read_orca_output+0x1d8)[0x2ba5c4959b98]
[ 3] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(call_orca+0xf0)[0x2ba5c495a0d0]
[ 4] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(calculate_QMMM+0xa67)[0x2ba5c496a647]
[ 5] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force_lowlevel+0x1629)[0x2ba5c487cdf9]
[ 6] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force_cutsVERLET+0x17bb)[0x2ba5c48cc31b]
[ 7] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_force+0x17f)[0x2ba5c48d02ef]
[ 8] /usr/local/g467d5-orca/lib/libmd_mpi_d.so.8(do_steep+0x5b3)[0x2ba5c48e4c33]
[ 9] mdrun_mpi_d(mdrunner+0x15f2)[0x40f172]
[10] mdrun_mpi_d(cmain+0x1a17)[0x433f67]
[11] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x2ba5c5d06830]
[12] mdrun_mpi_d(_start+0x29)[0x4072b9]
*** End of error message ***
Segmentation fault (core dumped)

I am clueless on where the error came from, would anyone have any insight?  Thank you.

Best regards,





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