Charm++: standalone mode (not using charmrun) Charm++> Running in Multicore mode: 1 threads 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: v6.7.0-0-g46f867c-namd-charm-6.7.0-build-2015-Dec-21-45876 [0] isomalloc.c> Disabling isomalloc because mmap() does not work CharmLB> Load balancer assumes all CPUs are same. Charm++> Running on 1 unique compute nodes (8-way SMP). Charm++> cpu topology info is gathered in 0.008 seconds. Info: Built with CUDA version 6050 Did not find +devices i,j,k,... argument, using all Pe 0 physical rank 0 binding to CUDA device 0 on John-PC: 'GeForce GT 720' Mem: 1024MB Rev: 3.5 Info: NAMD 2.11 for Win64-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. Comp. Chem. 26:1781-1802 (2005) Info: in all publications reporting results obtained with NAMD. Info: Info: Based on Charm++/Converse 60700 for multicore-win64 Info: Built Mon, Dec 21, 2015 10:32:11 AM 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 0.279 s Info: 23.8203 MB of memory in use based on GetProcessMemoryInfo Info: Configuration file is ubq_ws_eq.conf Info: Working in the current directory C:\Program Files (x86)\University of Illinois\VMD\namd-tutorial-files\1-2-sphere TCL: Suspending until startup complete. Info: SIMULATION PARAMETERS: Info: TIMESTEP 2 Info: NUMBER OF STEPS 0 Info: STEPS PER CYCLE 10 Info: LOAD BALANCER Centralized Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT Info: LDB PERIOD 2000 steps Info: FIRST LDB TIMESTEP 50 Info: LAST LDB TIMESTEP -1 Info: LDB BACKGROUND SCALING 1 Info: HOM 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 1 Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED Info: DCD FILENAME ubq_ws_eq.dcd Info: DCD FREQUENCY 250 Info: DCD FIRST STEP 250 Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT Info: NO VELOCITY DCD OUTPUT Info: NO FORCE DCD OUTPUT Info: OUTPUT FILENAME ubq_ws_eq Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME ubq_ws_eq.restart Info: RESTART FREQUENCY 500 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 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 16.5 Info: ENERGY OUTPUT STEPS 100 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 1000 Info: PRESSURE OUTPUT STEPS 100 Info: SPHERICAL BOUNDARY CONDITIONS ACTIVE Info: RADIUS #1 26 Info: FORCE CONSTANT #1 10 Info: EXPONENT #1 2 Info: SPHERE BOUNDARY CENTER(30.3082, 28.805, 15.354) Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 310 Info: LANGEVIN USING BBK INTEGRATOR Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS 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-008 Info: MAX ITERATIONS : 100 Info: RIGID WATER USING SETTLE ALGORITHM Info: RANDOM NUMBER SEED 1452810161 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB ../common/ubq_ws.pdb Info: STRUCTURE FILE ../common/ubq_ws.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS ../common/par_all27_prot_lipid.inp Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: SUMMARY OF PARAMETERS: Info: 180 BONDS Info: 447 ANGLES Info: 566 DIHEDRAL Info: 46 IMPROPER Info: 6 CROSSTERM Info: 119 VDW Info: 0 VDW_PAIRS Info: 0 NBTHOLE_PAIRS Info: TIME FOR READING PSF FILE: 0.0420001 Info: TIME FOR READING PDB FILE: 0.0109999 Info: Info: **************************** Info: STRUCTURE SUMMARY: Info: 6682 ATOMS Info: 4871 BONDS Info: 4074 ANGLES Info: 3293 DIHEDRALS Info: 204 IMPROPERS Info: 74 CROSSTERMS Info: 0 EXCLUSIONS Info: 6080 RIGID BONDS Info: 13966 DEGREES OF FREEDOM Info: 2419 HYDROGEN GROUPS Info: 4 ATOMS IN LARGEST HYDROGEN GROUP Info: 2419 MIGRATION GROUPS Info: 4 ATOMS IN LARGEST MIGRATION GROUP Info: TOTAL MASS = 41298.8 amu Info: TOTAL CHARGE = 1.00955e-006 e Info: ***************************** Info: Info: Entering startup at 0.353 s, 26.1719 MB of memory in use Info: Startup phase 0 took 0 s, 26.1719 MB of memory in use Info: ADDED 12209 IMPLICIT EXCLUSIONS Info: Startup phase 1 took 0.00300002 s, 27.625 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 ENERGY: 3.38813e-021 AT 11.8295 Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 5.45773e-014 AT 11.9138 Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 8.47033e-022 AT 11.9138 Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.6856e-015 AT 11.9138 Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000290274 AT 0.251946 Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 9.86076e-032 AT 11.8295 Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.75473e-014 AT 11.9138 Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 4.62223e-032 AT 11.9138 Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 2.12237e-015 AT 11.9138 Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946 Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 4.1359e-025 AT 11.8295 Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-015 AT 11.9138 Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 3.87741e-026 AT 11.9138 Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 5.97409e-016 AT 11.9138 Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946 Info: Updated CUDA LJ table with 119 x 119 elements. Info: Updated CUDA force table with 4096 elements. Info: Startup phase 2 took 0.095 s, 89.6992 MB of memory in use Info: Startup phase 3 took 0 s, 89.6992 MB of memory in use Info: Startup phase 4 took 0 s, 89.6992 MB of memory in use Info: Startup phase 5 took 0 s, 89.6992 MB of memory in use Info: PATCH GRID IS 3 BY 3 BY 3 Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY Info: REMOVING COM VELOCITY 0.0185738 0.0972739 -0.0312788 Info: LARGEST PATCH (13) HAS 500 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 0.00300002 s, 91.0156 MB of memory in use Info: Startup phase 7 took 0 s, 91.0156 MB of memory in use Info: Startup phase 8 took 0 s, 91.0156 MB of memory in use LDB: Central LB being created... Info: Startup phase 9 took 0 s, 91.0156 MB of memory in use Info: CREATING 381 COMPUTE OBJECTS CUDA device 0 stream priority range 0 -1 Info: Found 213 unique exclusion lists needing 616 bytes Pe 0 hosts 0 local and 27 remote patches for pe 0 Info: Startup phase 10 took 0.00399995 s, 92.5664 MB of memory in use Info: Startup phase 11 took 0 s, 92.5664 MB of memory in use Info: Startup phase 12 took 0 s, 96.5352 MB of memory in use Info: Finished startup at 0.458 s, 96.5352 MB of memory in use TCL: Minimizing for 100 steps