[gmx-users] QM/MM-ORCA Point Charge Correction Error (Zoe Chan)

Groenhof, Gerrit ggroenh at gwdg.de
Thu Nov 30 08:01:20 CET 2017


Does it run with the cutoff-scheme=group? 


After trying a few different settings of .mdp, I found that "cutoff-scheme = Verlet" and "QMMMscheme = ONIOM" were causing the error.  Would you have any idea how were these two settings linked to the generation of ".pc" file, and what would you suggest if I have to run under ONIOM?

Thank you.

Best regards,


From: CHAN, Zoe ZC [Student] <zoe.zc.chan at connect.polyu.hk>
Sent: 27 November 2017 18:23
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] QM/MM-ORCA Point Charge Correction Error (Zoe Chan)

Dear Gerrit,

Thank you very much for your prompt reply.
I?ve tried to run the simulation with wenjin?s tutorial and it passed the point charge correction step with no problem. I compared the ?.out? output files of my protein and of the tutorial peptide, I noticed there?s a line ?%pointcharges ?peptide.pc?? at the end of the input file section, I guess it shows that the basename has been linked to the ?.pc? point charge file instead of the default name ?temp.pc?, and it?s missing in my protein?s output file. Would that have possibly caused the crash?
Again, thank you for your help.

Best regards,

On 27 Nov 2017, at 6:11 PM, Groenhof, Gerrit <ggroenh at gwdg.de<mailto:ggroenh at gwdg.de>> wrote:

>From the error message it seems that ORCA program crashes. Unfortunately, Orca is no longer supported, which means that if the ORCA's input or anything else has changed, the gromacs interface may fail.

What you could try is to use the version of ORCA that others have used before.



Content-Type: text/plain; charset="iso-8859-1"

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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