Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 12 threads (PEs)
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Converse/Charm++ Commit ID: 
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 hosts (1 sockets x 6 cores x 2 PUs = 12-way SMP)
Charm++> cpu topology info is gathered in 0.000 seconds.
Info: Built with CUDA version 11000
Did not find +devices i,j,k,... argument, using all
Pe 0 physical rank 0 will use CUDA device of pe 8
Pe 10 physical rank 10 will use CUDA device of pe 8
Pe 3 physical rank 3 will use CUDA device of pe 8
Pe 11 physical rank 11 will use CUDA device of pe 8
Pe 4 physical rank 4 will use CUDA device of pe 8
Pe 6 physical rank 6 will use CUDA device of pe 8
Pe 9 physical rank 9 will use CUDA device of pe 8
Pe 5 physical rank 5 will use CUDA device of pe 8
Pe 2 physical rank 2 will use CUDA device of pe 8
Pe 7 physical rank 7 will use CUDA device of pe 8
Pe 8 physical rank 8 binding to CUDA device 0 on werkubuntu: 'NVIDIA GeForce GT 1030'  Mem: 1993MB  Rev: 6.1  PCI: 0:1:0
Pe 1 physical rank 1 will use CUDA device of pe 8
Info: NAMD 3.0alpha13 for Linux-x86_64-multicore-CUDA
Info: 
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info: 
Info: Please cite Phillips et al., J. Chem. Phys. 153:044130 (2020) doi:10.1063/5.0014475
Info: in all publications reporting results obtained with NAMD.
Info: 
Info: Based on Charm++/Converse 70000 for multicore-linux-x86_64-gcc
Info: Built Sun Jul 24 04:02:17 CDT 2022 by dhardy on athine.ks.uiuc.edu
Info: 1 NAMD  3.0alpha13  Linux-x86_64-multicore-CUDA  12    werkubuntu  gert
Info: Running on 12 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.290257 s
Info: 0 MB of memory in use based on /proc/self/stat
Info: Using bitfields in atom data structures.
Info:   sizeof( CompAtom )    = 32
Info:   sizeof( CompAtomExt ) = 8
CkLoopLib is used in SMP with simple dynamic scheduling (converse-level notification)
Info: Configuration file is QMMM-Min.conf
Info: Working in the current directory /home/gert/onedrive/ubuntu_werk/namd_vmd/junk/CBM_QM/run
TCL: Suspending until startup complete.
Warning: The following variables were set in the
Warning: configuration file but will be ignored:
Warning:    ionConcentration (GBIS)
Warning:    alphaCutoff (GBIS)
Info: EXTENDED SYSTEM FILE   QMMM-Min.xsc
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               0.5
Info: NUMBER OF STEPS        0
Info: STEPS PER CYCLE        1
Info: PERIODIC CELL BASIS 1  58.8481 0 0
Info: PERIODIC CELL BASIS 2  0 55.5702 0
Info: PERIODIC CELL BASIS 3  0 0 69.6404
Info: PERIODIC CELL CENTER   1.10762 0.431464 1.59686
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCER  Centralized
Info: LOAD BALANCING STRATEGY  New Load Balancers -- DEFAULT
Info: LDB PERIOD             200 steps
Info: FIRST LDB TIMESTEP     5
Info: LAST LDB TIMESTEP     -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MIN ATOMS PER PATCH    40
Info: EMPTY PATCH LOAD       40 ATOMS
Info: INITIAL TEMPERATURE    0
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC             1
Info: EXCLUDE                SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 1
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME           QMMM-Min.dcd
Info: DCD FREQUENCY          1
Info: DCD FIRST STEP         1
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME           QMMM-Min.xst
Info: XST FREQUENCY          1
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME        QMMM-Min
Info: RESTART FILENAME       QMMM-Min.restart
Info: RESTART FREQUENCY      1
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON           10
Info: SWITCHING OFF          12
Info: PAIRLIST DISTANCE      14
Info: PAIRLIST SHRINK RATE   0.01
Info: PAIRLIST GROW RATE     0.01
Info: PAIRLIST TRIGGER       0.3
Info: PAIRLISTS PER CYCLE    2
Info: PAIRLISTS ENABLED
Info: MARGIN                 0.495
Info: HYDROGEN GROUP CUTOFF  2.5
Info: PATCH DIMENSION        16.995
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    1
Info: PRESSURE OUTPUT STEPS  1
Info: HARMONIC CONSTRAINTS ACTIVE
Info: HARMONIC CONS EXP      2
Info: HARMONIC CONS SCALING  2
Info: QM FORCES ACTIVE
Info: QM PDB PARAMETER FILE: CBM_QM_QwikMD_qm-input.pdb
Info: QM SOFTWARE: MOPAC
Info: QM ATOM CHARGES FROM QM SOFTWARE: MULLIKEN
Info: QM EXECUTABLE PATH: /Scr/rcbernardi-new/Software/mopac/MOPAC2016.exe
Info: QM COLUMN: beta
Info: QM BOND COLUMN: occ
Info: QM WILL DETECT BONDS BETWEEN QM AND MM ATOMS.
Info: QM-MM BOND SCHEME: Charge Shift.
Info: QM BASE DIRECTORY: /home/gert/onedrive/ubuntu_werk/namd_vmd/junk/CBM_QM/run/qmmm_exec/QMMM-Min
Info: QM CONFIG LINE: PM7 XYZ T=2M 1SCF MOZYME CUTOFF=9.0 AUX LET GRAD QMMM GEO-OK
Info: QM CONFIG LINE: Test System
Info: QM POINT CHARGES WILL BE SELECTED EVERY 1 STEPS.
Info: QM Point Charge Switching: ON.
Info: QM Point Charge SCHEME: round.
Info: QM executions per node: 1
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE   0
Info: LANGEVIN USING BBK INTEGRATOR
Info: LANGEVIN DAMPING COEFFICIENT IS 50 INVERSE PS
Info: LANGEVIN DYNAMICS APPLIED TO HYDROGENS
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info:        TARGET PRESSURE IS 1.01325 BAR
Info:     OSCILLATION PERIOD IS 200 FS
Info:             DECAY TIME IS 100 FS
Info:     PISTON TEMPERATURE IS 273 K
Info:       PRESSURE CONTROL IS GROUP-BASED
Info:    INITIAL STRAIN RATE IS 2.79525e-05 2.79525e-05 2.79525e-05
Info:       CELL FLUCTUATION IS ISOTROPIC
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE               1e-06
Info: PME EWALD COEFFICIENT       0.257952
Info: PME INTERPOLATION ORDER     4
Info: PME GRID DIMENSIONS         60 56 72
Info: PME MAXIMUM GRID SPACING    1
Info: Attempting to read FFTW data from FFTW_NAMD_3.0alpha13_Linux-x86_64-multicore-CUDA.txt
Info: Optimizing 6 FFT steps.  1... 2... 3... 4... 5... 6...   Done.
Info: Writing FFTW data to FFTW_NAMD_3.0alpha13_Linux-x86_64-multicore-CUDA.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY      1
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RANDOM NUMBER SEED     1662370743
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         CBM_QM_QwikMD.pdb
Info: STRUCTURE FILE         CBM_QM_QwikMD.psf
Info: PARAMETER file: CHARMM format! 
Info: PARAMETERS             Retinal_schiff_based_qwikmd.str
Info: PARAMETERS             toppar_water_ions_namd.str
Info: PARAMETERS             toppar_all36_carb_glycopeptide.str
Info: PARAMETERS             par_all36_lipid.prm
Info: PARAMETERS             par_all36_na.prm
Info: PARAMETERS             par_all36_prot.prm
Info: PARAMETERS             par_all36_carb.prm
Info: PARAMETERS             par_all36_cgenff.prm
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SKIPPING rtf SECTION IN STREAM FILE
Info: SUMMARY OF PARAMETERS:
Info: 942 BONDS
Info: 2731 ANGLES
Info: 6593 DIHEDRAL
Info: 211 IMPROPER
Info: 6 CROSSTERM
Info: 357 VDW
Info: 6 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PSF FILE: 0.528785
Info: Reading pdb file CBM_QM_QwikMD.pdb
Info: TIME FOR READING PDB FILE: 0.0329902
Info: 
FATAL ERROR: QM forces are not compatible with CUDA at this time
FATAL ERROR: QM forces are not compatible with CUDA at this time
[Partition 0][Node 0] End of program