Charm++> No provisioning arguments specified. Running with a single PE. Use +auto-provision to fully subscribe resources or +p1 to silence this message. Charm++: standalone mode (not using charmrun) Charm++> Running in Multicore mode: 1 threads (PEs) Charm++> Using recursive bisection (scheme 3) for topology aware partitions Charm++ warning> fences and atomic operations not available in native assembly Converse/Charm++ Commit ID: v6.10.2-0-g7bf00fa-namd-charm-6.10.2-build-2020-Aug-05-556 Charm++> Disabling isomalloc because mmap() does not work. 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 0.007 seconds. Info: NAMD 2.14 for Win64-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. 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 61002 for multicore-win64 Info: Built Wed, Aug 05, 2020 1:08:15 PM by jim on europa Info: Running on 1 processors, 1 nodes, 1 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.00899982 s CkLoopLib is used in SMP with simple dynamic scheduling (converse-level notification) Info: 2.3125 MB of memory in use based on GetProcessMemoryInfo Info: Configuration file is water.namd Info: Working in the current directory C:\NAMD_2.14_Win64-multicore\16\R TCL: Suspending until startup complete. Info: Changed directory to ./ Warning: The parameter fullElectFrequency now defaults to nonbondedFreq (1) rather than stepsPerCycle. Info: SIMULATION PARAMETERS: Info: TIMESTEP 2 Info: NUMBER OF STEPS 10000 Info: STEPS PER CYCLE 20 Info: PERIODIC CELL BASIS 1 -30 0 0 Info: PERIODIC CELL BASIS 2 0 -30 0 Info: PERIODIC CELL BASIS 3 -0 -0 180 Info: PERIODIC CELL CENTER -10 -10 100.224 Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT. Info: WRAPPING TO IMAGE NEAREST TO PERIODIC CELL CENTER. Info: LOAD BALANCER Centralized Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT Info: LDB PERIOD 4000 steps Info: FIRST LDB TIMESTEP 100 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 310 Info: CENTER OF MASS MOVING INITIALLY? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 ELECTROSTATICS SCALED BY 0.833333 Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED Info: DCD FILENAME md_water_out.dcd Info: DCD FREQUENCY 500 Info: DCD FIRST STEP 500 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT Info: NO VELOCITY DCD OUTPUT Info: NO FORCE DCD OUTPUT Info: OUTPUT FILENAME md_water_out.pdb Info: RESTART FILENAME md_water_out.rst Info: RESTART FREQUENCY 1000 Info: BINARY RESTART FILES WILL BE USED Info: SWITCHING ACTIVE Info: SWITCHING ON 12 Info: SWITCHING OFF 14 Info: PAIRLIST DISTANCE 16 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 1 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 19.5 Info: ENERGY OUTPUT STEPS 500 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 500 Info: PRESSURE OUTPUT STEPS 500 Info: FIXED ATOMS ACTIVE Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 310 Info: LANGEVIN USING BBK INTEGRATOR Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS Warning: Option useGroupPressure is being enabled due to pressure control with rigidBonds. Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE Info: TARGET PRESSURE IS 1.01325 BAR Info: OSCILLATION PERIOD IS 100 FS Info: DECAY TIME IS 50 FS Info: PISTON TEMPERATURE IS 310 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 0.219398 Info: PME INTERPOLATION ORDER 4 Info: PME GRID DIMENSIONS 50 50 180 Info: PME MAXIMUM GRID SPACING 1.5 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: RIGID BONDS TO HYDROGEN : ALL Info: ERROR TOLERANCE : 1e-08 Info: MAX ITERATIONS : 500 Info: RIGID WATER USING SETTLE ALGORITHM Info: RANDOM NUMBER SEED 1653127960 Info: USE HYDROGEN BONDS? NO Info: Using AMBER format force field! Info: AMBER PARM FILE root_m_vac.prmtop Info: AMBER COORDINATE FILE root_m_vac.rst7 Info: Exclusions will be read from PARM file! Info: SCNB (VDW SCALING) 2 Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: BINARY COORDINATES min_all_out.rst.coor Reading parm file (root_m_vac.prmtop) ... PARM file in AMBER 7 format Warning: Skipping ATOMIC_NUMBER in parm file while seeking MASS. Warning: Skipping SCEE_SCALE_FACTOR in parm file while seeking SOLTY. Warning: Skipping SCNB_SCALE_FACTOR in parm file while seeking SOLTY. Info: SUMMARY OF PARAMETERS: Info: 41 BONDS Info: 86 ANGLES Info: 55 DIHEDRAL Info: 0 IMPROPER Info: 0 CROSSTERM Info: 0 VDW Info: 120 VDW_PAIRS Info: 0 NBTHOLE_PAIRS Info: TIME FOR READING PDB FILE: 0 Info: Info: **************************** Info: STRUCTURE SUMMARY: Info: 1941 ATOMS Info: 2094 BONDS Info: 3800 ANGLES Info: 7565 DIHEDRALS Info: 0 IMPROPERS Info: 0 CROSSTERMS Info: 10788 EXCLUSIONS Info: 1941 FIXED ATOMS Info: 685 RIGID BONDS Info: 685 RIGID BONDS BETWEEN FIXED ATOMS Info: 0 DEGREES OF FREEDOM Info: 1256 HYDROGEN GROUPS Info: 4 ATOMS IN LARGEST HYDROGEN GROUP Info: 1256 MIGRATION GROUPS Info: 4 ATOMS IN LARGEST MIGRATION GROUP Info: 1256 HYDROGEN GROUPS WITH ALL ATOMS FIXED Info: TOTAL MASS = 18851 amu Info: TOTAL CHARGE = -60 e Info: MASS DENSITY = 0.193231 g/cm^3 Info: ATOM DENSITY = 0.0119815 atoms/A^3 Info: ***************************** Info: Reading from binary file min_all_out.rst.coor Info: Info: Entering startup at 0.0379999 s, 3.90625 MB of memory in use Info: Startup phase 0 took 0 s, 3.90625 MB of memory in use Info: ADDED 0 IMPLICIT EXCLUSIONS Info: Startup phase 1 took 0.00200009 s, 4.48047 MB of memory in use Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 2.64698e-23 AT 13.9261 Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 3.03582e-16 AT 13.9261 Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000290477 AT 0.251946 Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 4.63221e-23 AT 13.9261 Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 1.36264e-15 AT 13.9261 Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000182292 AT 13.962 Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 4.93038e-32 AT 13.7818 Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 2.75256e-14 AT 13.9261 Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 3.08149e-33 AT 13.9261 Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 1.25762e-15 AT 13.9261 Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946 Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 1.03398e-25 AT 13.8542 Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 2.80645e-15 AT 13.9261 Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 9.69352e-27 AT 13.9261 Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 5.26168e-16 AT 13.9261 Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00165469 AT 12.1218 Info: Startup phase 2 took 0.000999928 s, 4.84375 MB of memory in use Info: Startup phase 3 took 0 s, 4.84375 MB of memory in use Info: Startup phase 4 took 0 s, 4.84375 MB of memory in use Info: Startup phase 5 took 0 s, 4.84375 MB of memory in use Info: PATCH GRID IS 1 (PERIODIC) BY 1 (PERIODIC) BY 9 (PERIODIC) Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY Info: REMOVING COM VELOCITY 0.070923 -0.147014 0.00901287 Info: LARGEST PATCH (0) HAS 325 ATOMS Info: TORUS A SIZE 1 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 0.000999928 s, 5.28125 MB of memory in use Info: PME using 1 and 1 processors for FFT and reciprocal sum. Info: PME GRID LOCATIONS: 0 Info: PME TRANS LOCATIONS: 0 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 0.00100017 s, 7.02344 MB of memory in use Info: Startup phase 8 took 0 s, 7.02344 MB of memory in use Info: Startup phase 9 took 0 s, 7.02344 MB of memory in use Info: Startup phase 10 took 0 s, 7.02344 MB of memory in use Info: Startup phase 11 took 0 s, 7.02344 MB of memory in use LDB: Central LB being created... Info: Startup phase 12 took 0 s, 7.02344 MB of memory in use Info: CREATING 185 COMPUTE OBJECTS Info: Startup phase 13 took 0.000999928 s, 7.53125 MB of memory in use Info: Startup phase 14 took 0 s, 7.53125 MB of memory in use Info: Startup phase 15 took 0 s, 8.93359 MB of memory in use Info: Finished startup at 0.0439999 s, 8.93359 MB of memory in use PRESSURE: 0 -581.277 28.8544 -763.872 15.1411 -548.79 -510.332 57.233 -64.8808 3281.94 GPRESSURE: 0 -581.277 28.8544 -763.872 15.1411 -548.79 -510.332 57.233 -64.8808 3281.94 ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG ENERGY: 0 0.0000 0.0000 0.0000 0.0000 -15383.4215 0.0000 0.0000 0.0000 0.0000 -15383.4215 -nan(ind) -15383.4215 -15383.4215 -nan(ind) 717.2920 717.2920 162000.0000 717.2920 717.2920