From: Oleksii Zdorevskyi (zdorevskyi_at_bitp.kiev.ua)
Date: Tue Sep 28 2021 - 14:11:06 CDT
My apologies, during the setup I have by chance deleted the selection of
the H2O2 molecule from the QM atoms. This resulted in the absence of
non-solvent atoms in the QM region, and, consequently, NAMD was not able
to determine its center of mass, and dumped. The absence or NAMD and ORCA
errors deceived me into that the problem was in the large number of
solvent molecules for LSS. I apologize for such an obvious mistake.
> Dear NAMD developers,
> I am facing an issue regarding the QM/MM setup of NAMD together with ORCA
> using Live solvent selection. Whenever I include a substantial number of
> water molecules to the QM region, my system firstly runs ok, but when it
> reaches the step for LSS exchange (listed in LSSfreq), the run immediately
> crashes with a Segmentation fault. I have tested this issue on different
> workstations and clusters with different amounts of memory allocation. On
> all the workstations, OpenMPI is configured correctly, so that NAMD+ORCA
> runs smoothly without LSS.
> To illustrate this problem with an example, please take a look at a very
> simple system of an H2O2 molecule in a water solution (71 water molecules
> in the QM region):
> Neither NAMD nor ORCA does not show any error, just a segmentation fault
> in the Slurm output file (qm_40c/slurm-719879.out):
> /var/spool/slurmd/job719879/slurm_script: line 19: 196326 Segmentation
> fault (core dumped) $NAMDDIR/namd2 +CmiSleepOnIdle qm1.conf > qm1.log
> Does NAMD implement some sophisticated calculations during the LSS
> exchange that clog up the memory immediately?
> Are there any limitations to the number of water molecules that can be
> chosen for LSS?
> Thanks in advance.
> Best regards,
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