Charm++: standalone mode (not using charmrun) Charm++> Running in Multicore mode: 12 threads Charm++> Using recursive bisection (scheme 3) for topology aware partitions Converse/Charm++ Commit ID: v6.7.1-0-gbdf6a1b-namd-charm-6.7.1-build-2016-Nov-07-136676 Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try run with '+isomalloc_sync'. CharmLB> Load balancer assumes all CPUs are same. Charm++> Running on 1 unique compute nodes (12-way SMP). Charm++> cpu topology info is gathered in 0.003 seconds. Info: NAMD 2.12 for Linux-x86_64-multicore 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. Comp. Chem. 26:1781-1802 (2005) Info: in all publications reporting results obtained with NAMD. Info: Info: Based on Charm++/Converse 60701 for multicore-linux64-iccstatic Info: Built Wed Dec 21 11:36:52 CST 2016 by jim on harare.ks.uiuc.edu Info: 1 NAMD 2.12 Linux-x86_64-multicore 12 minerva17.ch.huji.ac.il kddubey Info: Running on 12 processors, 1 nodes, 1 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.0233369 s CkLoopLib is used in SMP with a simple dynamic scheduling (converse-level notification) but not using node-level queue Info: 769.977 MB of memory in use based on /proc/self/stat Info: Configuration file is config.ORCA.namd Info: Working in the current directory /home/kddubey/Downloads/NAMD-QM-MM/Example1 TCL: Suspending until startup complete. Info: SIMULATION PARAMETERS: Info: TIMESTEP 0.5 Info: NUMBER OF STEPS 0 Info: STEPS PER CYCLE 1 Info: PERIODIC CELL BASIS 1 29 0 0 Info: PERIODIC CELL BASIS 2 0 34 0 Info: PERIODIC CELL BASIS 3 0 0 28 Info: PERIODIC CELL CENTER -0.021 0.008 0.108 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: INITIAL TEMPERATURE 300 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 PolyAla_out.dcd Info: DCD FREQUENCY 1 Info: DCD FIRST STEP 1 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME PolyAla_out.xst Info: XST FREQUENCY 1 Info: NO VELOCITY DCD OUTPUT Info: NO FORCE DCD OUTPUT Info: OUTPUT FILENAME PolyAla_out Info: RESTART FILENAME PolyAla_out.restart Info: RESTART FREQUENCY 100 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: QM FORCES ACTIVE Info: QM PDB PARAMETER FILE: PolyAla-qm.pdb Info: QM SOFTWARE: orca Info: QM ATOM CHARGES FROM QM SOFTWARE: MULLIKEN Info: QM EXECUTABLE PATH: /home/dodik/PROGRAMS/orca_3_0_3_linux_x86-64/orca 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/kddubey/Downloads/NAMD-QM-MM/Example1/QMMM Info: QM CONFIG LINE: ! B3LYP 6-31G Grid4 PAL4 EnGrad TightSCF Info: QM CONFIG LINE: %%output PrintLevel Mini Print[ P_Mulliken ] 1 Print[P_AtCharges_M] 1 end Info: QM POINT CHARGES WILL BE SELECTED EVERY 1 STEPS. Info: QM Point Charge Switching: ON. Info: QM Point Charge SCHEME: none. Info: QM executions per node: 1 Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 300 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 300 K Info: PRESSURE CONTROL IS GROUP-BASED Info: INITIAL STRAIN RATE IS 0 0 0 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 32 36 28 Info: PME MAXIMUM GRID SPACING 1 Info: Attempting to read FFTW data from FFTW_NAMD_2.12_Linux-x86_64-multicore.txt Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done. Info: Writing FFTW data to FFTW_NAMD_2.12_Linux-x86_64-multicore.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 7910881 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB PolyAla.pdb Info: STRUCTURE FILE PolyAla.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS CHARMpars/toppar_all36_carb_glycopeptide.str Info: PARAMETERS CHARMpars/toppar_water_ions_namd.str Info: PARAMETERS CHARMpars/toppar_all36_na_nad_ppi_gdp_gtp.str Info: PARAMETERS CHARMpars/par_all36_carb.prm Info: PARAMETERS CHARMpars/par_all36_cgenff.prm Info: PARAMETERS CHARMpars/par_all36_lipid.prm Info: PARAMETERS CHARMpars/par_all36_na.prm Info: PARAMETERS CHARMpars/par_all36_prot.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: 937 BONDS Info: 2734 ANGLES Info: 6671 DIHEDRAL Info: 203 IMPROPER Info: 6 CROSSTERM Info: 357 VDW Info: 6 VDW_PAIRS Info: 0 NBTHOLE_PAIRS Info: TIME FOR READING PSF FILE: 0.0288281 Info: Reading pdb file PolyAla.pdb Info: TIME FOR READING PDB FILE: 0.00901699 Info: Info: Using the following PDB file for QM parameters: PolyAla-qm.pdb Info: Number of QM atoms (excluding Dummy atoms): 20 Info: We found 2 QM-MM bonds. Info: Applying user defined multiplicity 1 to QM group ID 1 Info: 1) Group ID: 1 ; Group size: 20 atoms ; Total charge: 0 Info: MM-QM pair: 24:30 -> Value (distance or ratio): 1.09 (QM Group 0 ID 1) Info: MM-QM pair: 50:44 -> Value (distance or ratio): 1.09 (QM Group 0 ID 1) Info: **************************** Info: STRUCTURE SUMMARY: Info: 2279 ATOMS Info: 1546 BONDS Info: 879 ANGLES Info: 199 DIHEDRALS Info: 15 IMPROPERS Info: 6 CROSSTERMS Info: 0 EXCLUSIONS Info: 6837 DEGREES OF FREEDOM Info: 773 HYDROGEN GROUPS Info: 4 ATOMS IN LARGEST HYDROGEN GROUP Info: 773 MIGRATION GROUPS Info: 4 ATOMS IN LARGEST MIGRATION GROUP Info: TOTAL MASS = 13773.9 amu Info: TOTAL CHARGE = 2.98023e-08 e Info: MASS DENSITY = 0.82848 g/cm^3 Info: ATOM DENSITY = 0.0825485 atoms/A^3 Info: ***************************** Info: Info: Entering startup at 4.33697 s, 869.863 MB of memory in use Info: Startup phase 0 took 0.000659943 s, 869.863 MB of memory in use Info: The QM region will remove 19 bonds, 31 angles, 37 dihedrals, 3 impropers and 1 crossterms. Info: ADDED 2624 IMPLICIT EXCLUSIONS Info: Startup phase 1 took 0.00261903 s, 870.008 MB of memory in use Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556 Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556 Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 4.59334e-32 AT 11.9974 Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 7.4108e-17 AT 11.9974 Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946 Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 1.53481e-26 AT 11.9974 Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.96691e-18 AT 11.9974 Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946 Info: Startup phase 2 took 0.00720906 s, 874.215 MB of memory in use Info: Startup phase 3 took 0.000648022 s, 874.215 MB of memory in use Info: Startup phase 4 took 0.00103307 s, 874.215 MB of memory in use Info: Startup phase 5 took 0.000618935 s, 874.215 MB of memory in use Info: PATCH GRID IS 3 (PERIODIC) BY 2 (PERIODIC) BY 1 (PERIODIC) Info: PATCH GRID IS 2-AWAY BY 1-AWAY BY 1-AWAY Info: REMOVING COM VELOCITY -0.188499 0.149382 0.0208025 Info: LARGEST PATCH (0) HAS 384 ATOMS Info: TORUS A SIZE 12 USING 0 Info: TORUS B SIZE 1 USING 0 Info: TORUS C SIZE 1 USING 0 Info: TORUS MINIMAL MESH SIZE IS 1 BY 1 BY 1 Info: Placed 100% of base nodes on same physical node as patch Info: Startup phase 6 took 0.00254107 s, 874.781 MB of memory in use Info: PME using 11 and 12 processors for FFT and reciprocal sum. Info: PME GRID LOCATIONS: 1 2 3 4 5 6 7 8 9 10 ... Info: PME TRANS LOCATIONS: 0 1 2 3 4 5 6 7 8 9 ... Info: PME USING 1 GRID NODES AND 1 TRANS NODES Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done. Info: Startup phase 7 took 0.00187087 s, 874.781 MB of memory in use Info: Startup phase 8 took 0.00146294 s, 874.781 MB of memory in use LDB: Central LB being created... Info: Startup phase 9 took 0.00138307 s, 874.781 MB of memory in use Info: CREATING 216 COMPUTE OBJECTS Info: useSync: 0 useProxySync: 0 Info: Startup phase 10 took 0.00880694 s, 874.781 MB of memory in use Info: Startup phase 11 took 0.000662088 s, 874.781 MB of memory in use Info: Startup phase 12 took 0.000201941 s, 874.781 MB of memory in use Info: Finished startup at 4.36668 s, 874.781 MB of memory in use TCL: Minimizing for 100 steps Info: List of ranks running QM simulations: 1.